How to run payroll for the first time

Running payroll for the first time is mostly about setting things up correctly. Once registrations, pay schedules and deposit dates are in place, each payroll follows the same steps. This guide walks through the set-up and the cycle.

By Hamza Fida, Chartered Accountant. Reviewed by Awais Jameel, Chartered Accountant. Checked against official sources on . 2 minute read.

Short answer

To run payroll, first register with the IRS and your state for withholding and unemployment tax. Each pay period, calculate gross pay, withhold federal and state income tax and the employee's 7.65% FICA, pay the net amount, and deposit the withheld taxes plus your 7.65% match on the IRS schedule. File Form 941 quarterly, Form 940 yearly, and Forms W-2 by January 31.

At a glance

Before the first payroll
EIN, state withholding and unemployment accounts, EFTPS
From each employee
Form W-4, state withholding form, Form I-9
Each pay period
Gross pay, withholding, net pay, tax deposit
Deposits
Monthly or semiweekly, as the IRS assigns
Quarterly
Form 941 and state returns
Yearly
Form 940, Forms W-2 and W-3 by January 31
How to run payroll for the first timeSteps: 1. Get an EIN; 2. Register with your state; 3. Enroll in EFTPS; 4. Collect employee forms; 5. Choose a pay schedule and a payroll system.THE PROCESS AT A GLANCEHow to run payroll for the first time1Get an EINThe business's federalemployer number2Register withyour stateFor state income taxwithholding, where thestate has an incometax, and for stateunemployment insurance3Enroll in EFTPSThe Treasury's freeelectronic system forfederal tax deposits4Collect employeeformsForm W-4, any statewithholding form, andForm I-95Choose a payschedule and apayroll systemWeekly, biweekly,semimonthly or monthly,within your state'srules on pay frequencyChecked against official sourcesTax BakersHow to run payroll for the first timeSteps: 1. Get an EIN; 2. Register with your state; 3. Enroll in EFTPS; 4. Collect employee forms; 5. Choose a pay schedule and a payroll system.THE PROCESS AT A GLANCEHow to run payroll for the firsttime1Get an EINThe business's federal employer number2Register with your stateFor state income tax withholding, where thestate has an income tax, and for stateunemployment insurance3Enroll in EFTPSThe Treasury's free electronic system forfederal tax deposits4Collect employee formsForm W-4, any state withholding form, andForm I-95Choose a pay schedule and apayroll systemWeekly, biweekly, semimonthly or monthly,within your state's rules on pay frequencyChecked against official sourcesTax Bakers
The process at a glance: 1. Get an EIN; 2. Register with your state; 3. Enroll in EFTPS; 4. Collect employee forms; 5. Choose a pay schedule and a payroll system.

What needs setting up before the first payroll?

  1. Get an EIN

    The business's federal employer number. See what an EIN is.

  2. Register with your state

    For state income tax withholding, where the state has an income tax, and for state unemployment insurance.

  3. Enroll in EFTPS

    The Treasury's free electronic system for federal tax deposits.

  4. Collect employee forms

    Form W-4, any state withholding form, and Form I-9. See hiring your first employee.

  5. Choose a pay schedule and a payroll system

    Weekly, biweekly, semimonthly or monthly, within your state's rules on pay frequency.

How do you get from gross pay to net pay?

StepExample, $4,000 monthly salary
Gross pay$4,000.00
Less Social Security, 6.2%- $248.00
Less Medicare, 1.45%- $58.00
Less federal income tax, from Form W-4 and IRS tablesvaries
Less state income tax, where applicablevaries
Less other deductions, such as retirement or health premiumsvaries
Net payWhat the employee receives

The employer also owes its own $306 of Social Security and Medicare for this pay, plus unemployment taxes. See payroll taxes explained.

Pre-tax benefits reduce taxable wages. See employee benefits tax treatment.

When are taxes deposited?

New employers generally start on the monthly schedule: taxes for a month are due by the 15th of the next month. Employers with larger past liabilities deposit semiweekly, and any employer that accumulates $100,000 or more of tax on one day deposits by the next business day. See how to pay the IRS. The IRS tells you your schedule each year.

Which returns follow?

  • Form 941, each quarter, reporting wages, withholding and FICA, by the last day of the month after the quarter.
  • Form 940, each year, for federal unemployment tax.
  • Forms W-2 and W-3, to employees and the Social Security Administration by January 31.
  • State returns for withholding and unemployment, on the state's schedule.

Each form is explained in Form 941, Form 940 and Forms W-2 and W-3.

Should you use payroll software?

For most small businesses, yes. Payroll services calculate withholding, make deposits and file returns, which removes the most common and costly errors: late deposits and wrong withholding. Check which filings and states the service covers.

What records must you keep?

Pay records, time records where required, Forms W-4, deposit confirmations and filed returns, for at least 4 years. See how long to keep business records.

Restaurants have extra tip reporting steps; see restaurant bookkeeping.

Rather not run payroll yourself?

We set up your payroll registrations, run each payroll, deposit taxes on time and file every federal and state payroll return.

Questions people ask

How do I run payroll for the first time?

Register with the IRS and your state, collect employee forms, then each period calculate gross pay, withhold taxes, pay net pay and deposit the taxes.

When are payroll taxes due?

On the monthly or semiweekly deposit schedule the IRS assigns. New employers usually start monthly, due by the 15th of the next month.

Which forms does an employer file?

Form 941 quarterly, Form 940 yearly, Forms W-2 and W-3 by January 31, plus state withholding and unemployment returns.

Do I need payroll software?

It is not required, but for most small businesses it prevents the most common errors with withholding, deposits and filings.

Sources

Every fee, date and rule on this page was taken from these official and primary sources.

  1. IRS Publication 15 (Circular E): Employer's Tax Guide
  2. IRS: Form 941, Employer's Quarterly Federal Tax Return
  3. IRS: Form 940, Employer's Annual Federal Unemployment (FUTA) Tax Return
  4. Social Security Administration: Contribution and benefit base, 2026

Rules and fees change. If you are reading this long after September 30, 2026, confirm the figures with the source before you rely on them.

More in Payroll and contractors

This guide is general information. It is not tax or legal advice for your situation.