Healthcare organizations are required to be HIPAA-compliant to protect patient information. While credit card processors themselves are generally exempt, those that provide additional functions, such as invoicing and booking management, are subject to HIPAA compliance for healthcare providers to legally use their payment service.
With this in mind, I evaluated top payment processors that offer the best solutions for healthcare providers.
The eight best healthcare payment processors are as follows:
- Square: Best fully HIPAA-compliant free merchant account
- Chase Payment Solutions®: Best for healthcare practices using InstaMed
- Stax: Cheapest credit card processing for established US healthcare providers
- PaymentCloud: Best for healthcare practices classified as high-risk
- Helcim: Best for free invoicing and billing services
- U.S. Bank Merchant Services: Best for healthcare practices using Salucro
- Ivy Pay: Best for small therapy practices
- Dharma Merchant Services: Best for practices processing more than $10,000 per month
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Top Healthcare Payment Processors Compared
*Note that payment processors DO NOT need to be HIPAA-compliant if they only function to accept credit card payments. However, using payment services like invoicing and billing will require payment processors to have HIPAA compliance.
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HIPAA Compliance for Payment Processing
The Health Insurance Portability and Accountability Act (HIPAA) was enacted into law in 1996 to protect patients’ privacy by setting standards for how their information is shared and stored. This encompasses any healthcare system that holds patient health information (PHI).
Patient health information is data collected by healthcare practices that include:
- The individual’s past, present, or future physical or mental health
- The provision of health care to the individual
- The past, present, or future payment for health care
Any software used by healthcare organizations needs to be HIPAA-compliant if it has access to personal health-related information. So, by default, simple credit card processing is not a HIPAA-covered activity.
However, if a payment processor comes with tools for storing customer information, then HIPAA compliance will be required before it can be used by a healthcare organization for tasks such as appointment bookings, invoicing, as well as storing health records.
Credit card payment processors can become PCI-compliant healthcare payment platforms by doing the following:
- Signing or entering into a business associate agreement (BAA) with healthcare providers. This is a written agreement that clearly states each party’s responsibilities when accessing and storing PHI.
- Offering a proprietary HIPAA-compliant invoicing and billing system like InstaMed and Salucro
On the other hand, merchant account and payment services providers that simply process credit card transactions on behalf of a healthcare provider are not required to be HIPAA-compliant but are expected to integrate with HIPAA-compliant EHR and have PCI Level 1 accreditation.
Merchant processors that are PCI Level 1-compliant undergo annual third-party security audits and quarterly network scanning and maintain an in-house internal compliance team. Learn more about PCI compliance.
Square: Best Fully HIPAA-compliant Free Merchant Account
Pros
- Multiple EHR integrations
- Free invoicing and website builder
- Waived chargeback fees
Cons
- Extended business hours support only
- Same-day funding with fee
- Account stability issues
Overview
Who should use it:
Small and new healthcare practices looking for free/affordable appointments and billing systems.
Why I like Square Payments:
Square is an all-in-one point of sale (POS) system that comes with a built-in payment processing service. Unlike popular alternatives PayPal or Stripe, Square is fully HIPAA-compliant—ready to sign a BAA with healthcare providers. Find out how Square stacks up against Stripe and PayPal.
Square can also be automatically set up to accept Health Savings Account (HSA) and Flexible Spending Account (FSA) debit cards upon signing up for a merchant account. There is no approval process involved, nor does it charge a monthly fee for using Square’s payment processing feature.
- Monthly fee: $0 to $69
- In-person transaction fee: 2.6% + 10 cents
- Invoicing: 3.3% + 30 cents
- Online transaction fee: 2.9% + 30 cents
- Recurring billing and card-on-file: 3.5% + 15 cents
- Keyed-in/Virtual terminal payments: 3.5% + 15 cents
- ACH/Bank transfers: 1% ($1 min)
- Chargeback fee: Waived up to $250 per month
- Full HIPAA compliance
- Integrates with Remedly and DrChrono EHR platforms
- Accepts HSA and FSA debit card payments
- Free aggregate merchant account An aggregate merchant account is a merchant account owned by the payment processor and shared by more than one merchant. It is pre-approved so there is no application process required but more susceptible to being frozen.
- Free basic appointment POS software and website builder
- Free invoicing and recurring billing
- Includes ACH payment processing
- Free next-day funding, same-day funding with fee
Square is an excellent choice for small and startup healthcare organizations. It even offers volume discounts for merchants that process more than $250,000 per year. However, Square’s customer support is also limited to extended business hours. There are also merchant services providers that can offer better interchange rates for fast-growing healthcare organizations.
Related reading:
- Find better rates from the cheapest credit card processors.
- Square tops our list of best free merchant accounts.
- Learn what is a merchant account.
Chase Payment Solutions®: Best for Healthcare Practices Using InstaMed
Pros
- Free same-day funding for Chase Business Checking account holders
- Native integration with InstaMed
- Free traditional merchant account
Cons
- Outright hardware purchase
- Nonrefundable chargeback fees
- Possible monthly fee for InstaMed integration
Overview
Who should use it:
Healthcare practices that use InstaMed for their EHR systems’ invoice and billing management should use a Chase merchant account.
Why I like Chase:
I chose Chase primarily for its native healthcare billing management platform. Chase owns the highly popular InstaMed, used by over 50% of healthcare providers for its seamless integration with almost any EHR and healthcare IT system. With InstaMed, merchants get to use Chase payment processing on a fully HIPAA-compliant and PCI Level 1 secure platform.
Chase Payment Solutions® is also among the few direct processors that work directly with small businesses and offers free same-day funding with a Chase Business Checking account. Only Square comes closest in comparison for this feature but will require an additional fee. There are no monthly fees for using the service (though InstaMed may charge a separate fee for monthly account maintenance), nor does it tie you into long-term contracts.
- Monthly fee: $0 to $15*
- In-person transaction fee: 2.6% + 10 cents
- Online transaction fee: 2.9% + 25 cents
- Keyed-in transaction fee: 3.5% + 10 cents
- ACH processing fee: $25 per month for 25 transactions, 15 cents for additional
- Chargeback fee: $25 to $100
*Merchants with a Chase Business Checking account are required to maintain a minimum balance of $2,000 or a monthly service fee of $15 will be imposed.
- Fully HIPAA-compliant when used via InstaMed
- Accepts HSA and FSA debit card payments
- Accepts ACH payments
- Automated payment processing and reconciliation
- Free traditional merchant account
- Free same-day funding
- Can reprogram compatible existing hardware
- 24/7 customer support
Chase Payment Solutions by itself is not HIPAA-compliant, but it offers healthcare practices seamless integration with InstaMed so merchants do not have to worry about prolonged system setup. However, if you want Chase for its free same-day funding feature, you will need to open a Chase Business Checking account and maintain a minimum balance of $2,000 per month.
Stax: Cheapest Credit Card Processor for Established US Healthcare Providers
Pros
- Wholesale interchange plus pricing
- Offers free credit card processing
- 24/7 customer support
Cons
- Requires Zapier to integrate with EHRs
- High monthly account fee
- Lacks same-day funding option
Overview
Who should use it:
Healthcare practices that regularly process large-volume transactions (at least $20,000 in card sales per month).
Why I like Stax:
Stax is our favorite credit card processor for fast-growing and established businesses with its wholesale interchange rates that provide merchants with access to all in-person and remote payment methods. While it has all the bells and whistles to help merchants manage customer information, Stax is not, by itself, a fully HIPAA-compliant merchant account services provider. Instead, it integrates with EHRs via Zapier and has safeguards in place to ensure that no patient information is saved in its system with PCI Level 1 security compliance.
Though not a direct processor like Chase, Stax also offers a traditional merchant account. Healthcare providers interested in using Stax will shoulder a monthly fee based on their annual processing volume. In general, I recommend it to businesses that regularly process card payments over $20,000 per month to maximize potential savings.
- Monthly fee: $99 to $199
- Card-present transaction fee: Interchange plus 8 cents
- Card-not-present transaction fee: Interchange plus 18 cents
- Chargeback fee: $25
- PCI Level 1 security compliance
- Integrates with Aesthetics EMR via Zapier
- Integrates with other EHRs via API
- Accepts HSA and FSA debit cards
- Wholesale interchange plus pricing
- All-in-one monthly fee for all payment types
- Next-day funding option
- 24/7 customer support
Stax comes with a wide range of payment processing options including a PCI Level 1 compliance that ensures the security of patient data. However, it lacks a ready integration with EHRs, which may cause delays in setting up your payment processing service. That said, high-volume and healthcare establishments with multiple locations and the resources to invest can significantly benefit from Stax’s management features.
PaymentCloud: Best for Healthcare Practices Classified as High-risk
Pros
- High approval rating for high-risk merchant accounts
- Seamless payment gateway integrations
- Waived early termination fees
Cons
- Additional monthly fee for virtual terminal
- Longer application and approval process
- No publicly disclosed pricing
Overview
Who should use it:
Healthcare practices that have been qualified as high-risk businesses.
Why I like PaymentCloud:
Some healthcare practices may struggle with getting approved for a normal merchant account for reasons like constant large ticket prices for services and a high volume of subscription-based sales. PaymentCloud works with a number of banks and boasts a 98% merchant account approval rate. It is both a payment gateway agnostic and a fully HIPAA-compliant merchant processor via BAA, so PaymentCloud can seamlessly integrate with most online payment processing software without disrupting your business during migration.
All high-risk merchant accounts are exclusive to one business, much like Chase and Stax, and will require merchants to go through an application process. PaymentCloud also stands out for its advanced fraud prevention tools to protect you from chargebacks and thousands of direct software integrations including EHRs. Most of all, merchants rave about PaymentCloud’s excellent customer service, providing you with a dedicated account manager from the time you start your application.
Learn more: High-risk merchant account
- Monthly fee: $10 to $45*
- Payment gateway fee: $15 per month (average)
- Virtual terminal: $15 to $45 per month
- Transaction fees:
- Low-risk: 2% to 3.1%
- Medium-risk: 2.3% to 3.4%
- High-risk: 2.7% to 4.3%
- Chargeback fee: $25
- Early termination fee: Waived
*Rates vary among industries and clients. Pricing is based on average mid- and high-risk merchant services.
- Fully HIPAA-compliant
- Thousands of direct integrations including EHRs
- Low monthly fees for high-risk merchant accounts
- Flexible transaction fee pricing
- Accepts HSA and FSA debit card payments
- Accepts e-check payments
- Advanced fraud prevention tools
- Can reprogram compatible existing hardware
- 24/7 customer support
PaymentCloud is particularly popular with telemedicine practices. Note that this will require you to set up an online payment service that involves a virtual terminal, for which PaymentCloud charges an additional monthly fee.
Helcim: Best for Free HIPAA-compliant Invoicing and Billing Services
Pros
- Automated volume discount
- Free access to all payment processing services
- Interchange plus pricing
Cons
- Add-on fees for AMEX transactions
- Mobile credit card reader is among the most expensive
- Limited back office integrations
Overview
Who should use it:
Growing healthcare practices looking for free invoicing and billing management tools
Why I like Helcim:
Helcim is a merchant services provider that offers businesses traditional merchant accounts. The free, more stable, and less prone to frozen funds merchant account immediately gives Helcim a clear advantage in this area over Square and even Stax. In addition, Helcim offers automated volume discounts and interchange plus pricing that ensures merchants always get the lowest rates.
As with Square, Helcim is also HIPAA-compliant by signing BAA with healthcare practices. Helcim allows merchants to use its invoicing and recurring billing management tools without any additional cost—another reason for clinics to choose to integrate with Helcim over other competitors. Healthcare B2B transactions such as filing and receiving reimbursement from health insurance companies can also benefit from Helcim’s level 2 and 3 data optimization.
- Monthly fee: $0
- Card-present fee: Interchange plus 0.15% + 6 cents to 0.4% + 8 cents
- Card-not-present fee: Interchange plus 0.15% + 15 cents to 0.50% + 25 cents
- American Express transactions: +0.10% + 10 cents
- Domestic ACH Transfers: 0.5% + 25 cents per transaction
- Hardware: $99 to $329
- Chargeback fee: $15 refundable
- HIPAA-compliant via BAA
- Interchange plus pricing, no monthly account fee
- Free traditional merchant account
- Automated volume discount
- Free access to virtual terminal, invoicing, and recurring billing management tools
- Secure card vault at no extra cost
- Accepts card and ACH payments
- Accepts HSA and FSA debit card payments
- Chargeback management and fraud prevention tools
- Online subscription with free customer portal
- Level 2 and 3 data optimization available for all merchant clients
- Free in-person and online surcharging program
While Helcim’s traditional merchant account is more stable, small and new businesses may struggle to get approved for one. Helcim’s limited plug and play integration may also mean that it will require a custom, developer-based setup to connect with EHRs.
U.S. Bank Merchant Services: Best for Healthcare Practices Using Salucro
Pros
- Free same-day funding
- No long-term contract even with hardware rental
- Proprietary HIPAA-compliant billing management platform
Cons
- Monthly account fee with flat rate pricing
- List of integrations not available on the provider website
- Hardware rental option with monthly insurance fee
Overview
Who should use it:
Healthcare practices that integrate their EHR systems with Salucro for invoice and billing management should use a U.S. Bank merchant account.
Why I like U.S. Bank Merchant Services:
U.S. Bank Merchant Services is a welcome addition to our list, joining Chase Merchant Services as the second direct processor that provides a merchant account directly to small businesses. Like Chase, U.S. Bank offers free same-day funding to merchants using its business bank account. Additionally, it also provides a proprietary HIPAA-compliant billing management platform, Salucro, which U.S. Bank recently acquired.
Salucro Healthcare Solutions, like InstaMed, is used for patient billing and payment collection by many healthcare institutions. The platform allows users to accept ACH, credit, debit, HSA and FSA cards, Zelle, Apple Pay, Google Pay, and other contactless payments. Do you have patients still paying with traditional checks? U.S. Bank can efficiently process paper checks via its Remote Deposit Capture (RDC) where users only need to take a photo of the check and send it directly to the bank for processing and funding within the day.
- Monthly fee: $0 to $99
- In-person transactions: 2.6% + 10 cents
- Keyed-in transactions: 3.5% + 15 cents
- Online transactions: 2.9% + 30 cents
- Online ordering: $0 to $49 per month
- Hardware: $20 per month to $34 per month + $4.95 insurance fee
- Setup fee: $0 to $99
- No long-term contracts even with hardware rental
- Proprietary HIPAA-compliant billing management platform
- Accepts card, ACH, and remote paper check deposits
- Mobile, online, and invoicing tools
- Option to rent card readers and payment terminals
- Free same-day funding
- 24/7 customer support
- Free surcharging and debit card optimization
U.S. Bank Merchant Services offers a free mobile plan that allows you to accept payments, It’s also great for accepting online payments using the patient-facing payment gateway. However, note that you will need to upgrade to a paid plan if you want an on-premise, in-person payment setup. U.S. Bank will also charge you a $99 setup fee.
Ivy Pay: Best for Therapists With a Small Practice
Pros
- EHR with built-in payment processing
- Mobile app for iOS and Android
- Free merchant account
Cons
- Limited use for licensed therapists
- Limited to text messaging notification
- Not compatible with other EHRs
Overview
Who should use it:
Therapists with small healthcare practices who use the Talk to Ivy app to manage patient schedules and profiles.
Why I like Ivy Pay:
Ivy Pay is a fully HIPAA-compliant payment processor exclusively designed for therapists using the Talk to Ivy referral service platform to connect with patients. Ivy Pay is mobile-based and compatible with both iOS and Android smartphones—download the app to connect with clients and link a valid bank account to start accepting payments. You can charge a patient’s saved credit or debit cards from your app. Funds are deposited to you the next day.
There are no monthly fees, and a simple flat rate is charged for each transaction (significantly lower compared with Square’s online rate of 2.9% + 30 cents). Like Square, Ivy Pay is easy to set up and exclusive to the provider’s POS system. This is why I recommend Ivy Pay and Talk to Ivy for therapists with small or solo practices that do not need complicated billing and invoicing features.
- Monthly fee: $0
- Transaction fee: 2.75%
- Cancellation fee: $0
- Fully HIPAA-compliant
- Built-in payment processor for Talk to Ivy referral services platform
- Mobile-based, remote payment processing
- Accepts HSA and FSA payments
- No long-term contracts
- No credit card reader required
For therapists who are starting out, Ivy Pay is a great option to start your practice without significant upfront costs. However, some merchants will find it easy to outgrow Ivy Pay’s features and will need to upgrade to a service that offers invoicing and recurring billing tools and more notification functionality options.
Dharma Merchant Services: Low-cost Credit Card Processing for Midsize Healthcare Providers
Pros
- Special discounted interchange-plus rates for healthcare services
- Free next-day funding for card-present transactions
- 24/7 customer support
Cons
- Surcharge fee for Amex transactions
- Add-on monthly fees for ACH and invoicing
- Charges for PCI noncompliance
Overview
Who should use it:
Growing or midsize healthcare practices that can get value from large volume transactions even with additional payment services costs and handle their annual PCI compliance.
Why I like Dharma Merchant Services:
Dharma Merchant Services provides a dedicated merchant account service for healthcare providers. I love that it offers low interchange plus transaction rates. There are no long-term contracts, but there are monthly account fees involved that are to be expected for traditional merchant account service providers that offer interchange plus pricing. And because Dharma is a fully HIPAA-compliant merchant service provider, it can integrate with most EHR systems.
Compared with Stax, Dharma offers significantly lower monthly account fees, although be aware of the additional monthly cost of using other payment services like invoicing, recurring billing, and accepting ACH payments. Dharma also charges for PCI noncompliance. I recommend Dharma for midsize healthcare providers that can handle these additional costs.
- Monthly account fee: $25
- Transaction fee: Interchange plus 0.15% + 8 cents
- Amex transaction fee: Interchange plus 0.25% + 8 cents
- High-volume transaction fee: Interchange plus 0.10% + 8 cents*
- ACH monthly fee: $25 + 40 cents per transaction
- Invoicing and recurring billing monthly fee: $10
- Chargeback fee: $25
- Account closure fee: $49
*For sales volume above $100,000 per month
- Fully HIPAA-compliant merchant account
- Likely integrates with most EHR systems
- Accepts FSA and HSA debit cards
- Free virtual terminal
- Free mobile POS app
- Compatible with Clover hardware
- Guaranteed 48-hour funding
- Next-day funding for card-present transactions
Dharma Merchant Services can integrate with any EHR system with a signed BAA but still consult with a Dharma representative to verify that it will work with your current healthcare service management system. Even with a fully HIPAA-compliant merchant account service, Dharma’s ranking in our evaluation was significantly affected by the potential add-on fees including incidentals such as PCI noncompliance and account closure.
How I Evaluated the Best Healthcare Payment Processors
I compared a dozen healthcare payment processors and evaluated them based on pricing, payment types, ease of use, and expert score. Compliance and transparency are the priorities in evaluating each criterion. I also invited our retail experts to weigh in with their knowledge of each merchant processor in our list.
Square emerged as the best healthcare payment solution in our evaluation, with a score of 4.55 out of 5 for its fully HIPAA-compliant payment processing and value for money for small healthcare providers. Other healthcare payment processors also made our list for their standout functionalities.
Click through the tabs below for a more detailed breakdown of our evaluation criteria:
25% of Overall Score
I took into consideration the monthly fees and hardware fees, as well as contract terms and costs for early cancellations. Square earned the highest score of 4.25 out of 5, followed by Helcim and Ivy Pay with 4 out of 5.
30% of Overall Score
25% of Overall Score
In this category, I included approval, setup, migration, customer service hours, deposit speed, and available integrations for evaluation. I gave premium points for healthcare payment solutions that offer the best EHR integrations. This time, Chase and U.S. Bank MS both led with a score of 4.75 out of 5.
20% of Overall Score
Our expert score category evaluated each provider in terms of transparency and value for money. I also considered scalability as well as popularity among healthcare providers. Most of our providers did well here, but Square earned a perfect score.
Healthcare Payment Processing Rubric
How to Choose a Healthcare Payment Solution
When choosing among healthcare payment processing companies, compliance should be the main priority. You should also look for providers that offer the most value for money in terms of payment features and fees.
- HIPAA compliance: Without a doubt a prerequisite and a deal-breaker for any merchant processor that aims to provide a healthcare merchant account with additional management features.
- Security: Avoid merchant processors that do not have PCI Level 1 security. Additionally, choose a healthcare payment solution that offers advanced fraud protection and detection tools to effectively prevent chargebacks.
- Integrations: Ideally, you will want to have a merchant processor that’s compatible with most popular EHR systems, including what you currently use. Apart from EHR systems, you should also consider integration capabilities with other business software such as ecommerce, accounting, and appointment management.
- Credit card processing fees: In general, you will want to choose a merchant processor that offers transparent pricing. As much as possible, opt for solutions that offer interchange plus rates and low (or free) monthly fees. Look out for incidental costs such as chargebacks and surcharges for using additional payment functionalities like invoicing, virtual terminals, and payment gateways.
Healthcare Payment Processors Frequently Asked Questions (FAQs)
A healthcare merchant account provides merchant services that are unique to healthcare service providers such as hospitals and private practices. Most of the time, merchant processors that offer these services also come with HIPAA compliance, particularly if they provide additional functions such as scheduling, invoicing, and ecommerce.
Medical clinics can use non-HIPAA-compliant payment processors for simple credit card payment processing. However, this means that there is no integration with your practice management system and EHRs, which can cost you extra time and resources to keep track of your finances.
No. PayPal, Stripe, and peer-to-peer payment processors like Zelle and Venmo are not HIPAA-compliant. These payment processors do not go into business associate agreements (BAAs) and also use client information for marketing purposes.
Bottom Line
Payment processing services for healthcare providers require strict PCI security and HIPAA compliance to protect patient information. Focus on value for money, as while cheap fees and free services can be tempting, the consequences of noncompliance can cost your business even more.
Of all the healthcare payment processing software in our list, Square goes above and beyond HIPAA compliance when it comes to its payment processing and management tools. It offers appointment POS and free ecommerce tools and integrates with well-known EHR platforms.