Healthcare payroll · September 20, 2026
Best payroll software for healthcare practices (2026)
Front desk, clinicians, and a payday that files. A practice OS is not a substitute for tax deposits.
By Gregory GreensteinUpdated September 20, 2026Affiliate disclosure
Practice payroll is still US payroll: W-2s, withholdings, deposits, and a Friday that does not bounce. The extra jobs are mixed exempt/hourly, 1099 locums, and a practice manager who will not finish a 400-person HCM. EHR and RCM are different products.
This ranking is for US independents and small groups — dental, medspa, PT, primary care — not a hospital system. Gusto publishes a bill. Square wins when the front desk already takes cards on Square. Paychex and ADP are quotes for offices whose broker already lives there.
Prices as of September 20, 2026. Classification of associates and locums is a legal question. This is not wage, benefits, or HIPAA advice.
The short list
Public list prices as of September 20, 2026. Promos change. Confirm on the vendor page before you buy.
| # | Product | Best for | Public starting price | Score |
|---|---|---|---|---|
| 1 | Gusto | Practices that want published pricing and a manager who can finish setup without an EHR lock-in | Simple $49/mo + $6/person; Plus $80 + $12; Premium $180 + $22. Contractor Only $35 + $6. Simple is single-state. | 8.5 |
| 2 | Square Payroll | Clinics already taking cards and bookings on Square | Full-service $35/mo + $6 per person paid that month. Contractor-only $6 per contractor paid, no base fee. | 8.2 |
| 3 | Paychex Flex | Offices whose CPA, 401(k), or workers’ comp already lives at Paychex | Quote-only. Packages are typically Flex Select, Pro, and Enterprise. Request PEPM, base, implementation, year-end, and benefits add-ons in writing. | 7.6 |
| 4 | ADP RUN | Practices whose lender or CPA already standardized on ADP | Quote-only. Packages are Essential, Enhanced, Complete, and HR Pro. ADP asks you to request pricing. | 7.5 |
01
Gusto
Practices that want published pricing and a manager who can finish setup without an EHR lock-in
Public pricing: Simple $49/mo + $6/person; Plus $80 + $12; Premium $180 + $22. Contractor Only $35 + $6. Simple is single-state.
Gusto public pricing (gusto.com/product/pricing), reviewed September 20, 2026.
Skip if
Your CPA or benefits broker already lives in Paychex or ADP and will not switch. Or the front desk already lives in Square and hours come off that login.
Why it ranks
- A practice manager can estimate eight W-2s on a napkin.
- Full-service US filings, with 1099s if locums are contractors — classification is on you.
- Benefits sit next to payday when you hire the first benefits-eligible associate.
- Pairs with QBO and Xero, where many practice books already live.
Watch-outs
- Simple is single-state. A second clinic in another state usually means Plus.
- Not an EHR. Tebra-class suites are a different job.
- PTO and on-call rules still have to be configured. Software files what you set up.
- Do not buy Premium for a three-operatory shop.
02
Square Payroll
Clinics already taking cards and bookings on Square
Public pricing: Full-service $35/mo + $6 per person paid that month. Contractor-only $6 per contractor paid, no base fee.
Square Payroll pricing (squareup.com/us/en/payroll/pricing), reviewed September 20, 2026.
Skip if
You are not on Square and do not plan to be. Payroll alone is cheaper to compare against Gusto without dragging in a new POS.
Why it ranks
- Hours can come from Square Team / Appointments instead of a third timesheet.
- Published math you can put next to Gusto — $35 + $6 vs $49 + $6.
- Same login family as the front-desk card.
- Contractor-only is honest if locums are 1099s — still a classification question.
Watch-outs
- Per-person fees apply in months you pay them. Seasonal assistants still show up.
- Multi-state and multi-EIN limits exist. Read Square’s current constraints.
- Benefits are partner add-ons, not the $35.
- If the practice OS already includes payroll, do not dual-stack Square for a $14 base-fee delta.
03
Paychex Flex
Offices whose CPA, 401(k), or workers’ comp already lives at Paychex
Public pricing: Quote-only. Packages are typically Flex Select, Pro, and Enterprise. Request PEPM, base, implementation, year-end, and benefits add-ons in writing.
Paychex official site (paychex.com), reviewed September 20, 2026. No national self-serve rate card.
Skip if
You want a napkin bill this Tuesday. Paychex is a conversation. Start with Gusto unless the relationship is the product.
Why it ranks
- The relationship is the product: retirement, workers’ comp, a local-ish contact.
- Useful when the broker will not move the 401(k).
- Full-service filings on standard small-business packages they advertise.
- See Paychex vs ADP and Gusto vs Paychex if you are arguing in a partner meeting.
Watch-outs
- You cannot compare Flex to Gusto Simple without a quote.
- Implementation and year-two fees are how teasers happen.
- Not an EHR.
- We do not treat third-party call quotes as list.
04
ADP RUN
Practices whose lender or CPA already standardized on ADP
Public pricing: Quote-only. Packages are Essential, Enhanced, Complete, and HR Pro. ADP asks you to request pricing.
ADP RUN pages, reviewed September 20, 2026.
Skip if
You do not have a written quote. Brand is not a rate card.
Why it ranks
- Boards and lenders already know the logo.
- A path into broader HCM if the group actually grows.
- Filings and garnishments are why the brand exists.
- See Gusto vs ADP RUN for the published fork.
Watch-outs
- No napkin. No comparison.
- Implementation is a project.
- Do not buy RUN to look like a hospital.
- Rippling is the IT fork — see Gusto vs Rippling payroll.
How we picked
The job is US practice payday: mixed staff, filings, and a manager who can finish setup. We scored published pricing honesty, Square adjacency, and quote friction. EHR/RCM suites stay off unless payroll is a first-class published product. AI scribes stay on Aiacent.