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Payroll software for doctors’ offices

OnPay helps healthcare providers save time and reduce payroll-related hassles. We make it easy to pay your staff, handle tax filings, and simplify your HR — all in one place.


Perfect for healthcare professionals

We know that patients are the most important thing for doctors and healthcare workers. That’s why OnPay’s full-service payroll and HR software streamlines everything so you can focus on providing great care. With OnPay, you can pay W-2 employees and 1099 contractors at rate, on any schedule – and add overtime if needed. Integration with popular back office software eliminates double-data entry and keeps your accountant happy, too.


The all-in-one payroll prescription

  • Automated tax filings and payments
  • Cloud-based and mobile-friendly software
  • Flexible levels of permission to assign payroll tasks
  • Pay by direct deposit, debit card, or check
  • Get support from real payroll pros by chat, phone, or email
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“I run a busy doctor’s office with little time to waste. Running payroll with OnPay literally takes me less than five minutes each pay period ⁠— for full-time employees and 1099s alike. It’s easy to add an end of year bonus as well. I couldn’t be happier.”

— Daniel A Lindenberg, MD PA


The cure of all of your administrative hassles

Simplify onboarding

Send offer letters electronically, and let new employees can self-onboard and e-sign HR docs all in the app. You can also even build onboarding workflows to make it easy to scale your staff.

Keep everyone organized

OnPay’s HR tools to help your practice stay organized (and compliant). Automate PTO accruals, assign personnel tasks, and keep employee paperwork securely stored in our document vault.

Sync benefits and workers’ comp

Look after the health and wellbeing of your staff, too. OnPay can serve as your broker of record for health benefits with all of the top carriers. You can even integrate a workers’ comp plan that syncs with payroll.

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Payroll services with clear pricing

With OnPay, you get just what the doctor ordered – transparent pricing. powerful software, and no hidden fees. Starting at just $40 + $6/person each month.

  • Unlimited monthly pay runs
  • One monthly fee for all the essentials
  • Free migration of prior wage and employee data
  • Award-winning customer support
  • Year-end W-2s and 1099s included


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Try the best payroll for doctors and healthcare practices

It’s easy to get started. Provide just a little information about your practice and we’ll handle the rest.

Payroll for doctors and healthcare practices FAQs

  • How long does it take to set up an account and start running payroll?

    You can get set up super fast – we’ll just need some basic details so our team can help assist you with your setup. And our in-house payroll experts will do all the heavy lifting — from setting up your dashboard to adding your clients and their employees. We’ll even enter any prior wages to make it easy to switch, and can have you up and running in a matter of days.

  • What do employees usually have access to when they log into OnPay?

    It depends on what you want them to have access to, but at a minimum your employees can see their pay stubs, personal information, 1099, or W-2, and can even request time off. Read more in our help guide.

  • Are you able to integrate with the time tracking software my medical practice uses?

    We understand that many medical practices and doctor’s offices use time tracking software, and chances are we’ll be able to integrate with yours. At the moment, OnPay can connect to QuickBooks Time, When I Work and Deputy, and this detailed integrations guide can help you learn more about the various services we sync with.

  • Does OnPay handle new hire reporting or take care of it for me?

    Yes! OnPay will report new hires to all fifty states and the District of Columbia. Typically, reporting on new hires is completed every Friday before the close of business.