FAQ
Questions, answered
plainly.
Thirty-six answers about payroll, benefits, embedding, the API, pricing and compliance. If yours is missing, the team answers from the Contact page.
(01)
Payroll
Can we pay 1099 contractors in the same run?
Yes. Contractors and W-2 employees run in one payroll. We file their 1099-NEC forms in January.
Do we touch the money?
No. Funds move between the employer's bank and our partner bank. Your app shows the status.
When does the money move?
For a Friday payday, the cut-off is Tuesday at 5 p.m. ET. We debit the employer's account two banking days before payday, on Wednesday, and deposits land on Friday at 6 a.m. in each employee's time zone.
What happens when a bank holiday falls on payday?
Payday moves to the banking day before, and the cut-off and debit move with it. Christmas 2026 falls on a Friday, so weekly employees are paid on Thursday, December 24, with the cut-off on Monday, Dec 21 and the debit on Tuesday, Dec 22.
Which pay frequencies can an employer run?
Weekly, biweekly, semi-monthly and monthly. Each pay schedule has its own cut-offs, debits and paydays, and the pay calendar in your app shows all four for the month ahead.
Can we run a bonus or a final paycheck outside the schedule?
Yes, as an off-cycle run: Bonus, Final paycheck or Correction. Approved by 2 p.m. ET, it is paid the same day. Bonuses are withheld at the 22% federal supplemental rate.
How do tips, commission and prevailing wage show up?
As their own line on the paystub, named the way your vertical names them: Tips for a restaurant, Commission + tips for a salon, Prevailing wage for a contractor. The math behind each line stays the same.
(02)
Benefits
Which benefits can employees enroll in?
Two medical plans, PPO 1500 and HDHP with an HSA, plus dental, vision, a 401(k) and life & AD&D. Employers can add four monthly stipends: wellness, remote, learning and commuter.
How does a plan choice reach the paystub?
Enrollment and payroll share one record. Pick a tier and the deduction, the employer share and the net pay change on the next paycheck. Marisol Vega moving from Employee to Family on the PPO pays $214.30 a week instead of $61.50, and her net goes from $1,284.60 to $1,177.11.
Are premiums taken before tax?
Medical, dental and vision premiums come out under Section 125, before federal income tax and FICA. 401(k) contributions come out before federal income tax only. Each line on the stub says which.
How does the carrier get the enrollment?
We send the carrier an EDI 834 file the same night. Marisol's enrollment left at 11 p.m. ET and was acknowledged at 11:04 p.m. ET.
What is earned wage access?
Employees can take part of what they've already earned before payday, instantly, with a $0 fee and no cost to the employer. The advance comes back as one line on Friday's stub: − Earned wage advance $49.20.
Do unused stipends roll over?
Yes, if the employer switches roll-over on, up to a cap they set. A $100 wellness stipend with a gym, a yoga class and running shoes on it still has $16.40 left on day 30.
(03)
Embedded
How long until a new employer runs payroll?
Eight business days, median: business verification, bank account check and prior payroll import.
Will our customers ever see the Payrun name?
Only if you want them to. Set poweredBy to false and the "Payroll powered by Payrun" line leaves the screen, the paystub PDF and the deposit email.
How much of the payroll UI do we build?
You choose one of three depths. Hosted flow: a link, our screens, your theme. Components: our React components inside your pages. API only: your screens, our math and filings.
What can the theme change?
Eleven tokens: color, radius, type, logo, the words your vertical uses and the powered-by line among them. Pass the theme once and it follows every screen, down to the paystub PDF and the deposit email.
Where do employees see their paystubs?
In your app, on its Payroll tab, in your colors. They also get a deposit email and a paystub PDF with your header, for example "Prepared by Shearline".
Can each vertical keep its own words?
Yes. A restaurant app says Orders and Tips, a dog daycare app says Bookings and Pups. The words are part of the theme, so the same payroll reads like your product in each.
(04)
Developers
What happens if an employer's debit fails?
We hold the run, send payroll.funding_failed to your webhook and retry the next banking day. Nobody is paid from a failed debit.
Is there a sandbox?
Yes, free with your API keys. The sandbox clock advances a test run to its next event, from cut-off to taxes filed, so you can test Friday on a Wednesday.
How is the API versioned?
By date. The current version is 2026-10-14. You pin a version and upgrade when you choose; every change is dated in the changelog, and breaking ones are marked.
Which webhooks can we subscribe to?
Eight events: payroll.approved, payroll.funded, payroll.funding_failed, paystub.issued, deposit.returned, tax_filing.submitted, tax_filing.accepted and enrollment.updated.
What happens when a deposit is returned?
The bank sends it back with a code, for example R03: no account, unable to locate. You receive deposit.returned, the employee is asked in your app to update their account, and the payment goes out again once it is fixed.
Which SDKs do you ship?
Node.js and Python, a Postman collection, and example apps on GitHub.
(05)
Pricing
Can we set our own price?
Yes. You bill your customers. We bill you per employee paid each month.
How is Payrun priced?
Per employee paid each month (PEPM). Launch is $6.40 up to 5,000 employees, with a $750 monthly minimum. Scale is $4.85 from 5,000 to 50,000, with a $4,000 minimum. Enterprise starts at $3.90 above 50,000.
Who counts as an employee paid?
Anyone who received a paycheck in the month. An employee on unpaid leave that month is not billed. Contractors are billed apart, at $1.90 per contractor paid.
Which add-ons cost extra?
Benefits administration is +$2.10 PEPM. Contractors are $1.90 per contractor paid. Earned wage access costs the employer nothing.
How much can we keep?
At 1,000 businesses with 18 employees each, on Scale, and an $11.00 resale price, you keep $1,328,400 a year. The pricing page lets you change both numbers.
(06)
Compliance
Who files the W-2s and quarterly 941s?
We do, under your customer's EIN, in every state and locality where they have employees. You never see a form.
Which states do you file in?
All 50 states and Washington, D.C., plus local taxes where they apply, such as New York City or Ohio cities and school districts. We register the employer, withhold, pay and file under its EIN.
Which forms do you file?
Form 941 every quarter and 940 every year, W-2 and W-3, 1099-NEC, state withholding and unemployment returns, new-hire reports and local returns. The next 941, for Q4 2026, is due on Monday, February 1, 2027.
Can you handle wage garnishments?
Yes. A child support order is added to the paystub as its own line, withheld after taxes and capped at the limit the order sets, for example 50% of disposable earnings. Switch it off and the line goes away.
Can an employer switch to Payrun in the middle of the year?
Yes. We import year-to-date wages, taxes and deductions from the previous provider, so the W-2 in January covers the whole year. The import is part of the eight business days before the first run.
Do you have a SOC 2 report?
Our SOC 2 Type II report is available on request. Data is encrypted at rest and in transit, funds are held by our partner bank, and staff access is role-based.