How to Do Payroll in Missouri: A Step-by-Step Guide

Last reviewed: July 2026

Missouri's headline rule is pay frequency: corporations have to pay wages semimonthly by statute, which surprises employers used to biweekly or monthly cycles elsewhere. Beyond that, the sequence is familiar, an EIN, two state accounts, and a set of forms collected before day one.

1. Get Your Federal EIN

Every payroll setup starts with a federal Employer Identification Number. Apply free at IRS.gov and you'll have it within about fifteen minutes. You'll need it for every state registration that follows, plus your business bank account and payroll software.

2. Register with Missouri Revenue

Register for a withholding account with the Missouri Department of Revenue. This lets you withhold Missouri income tax from employee paychecks and remit it on the schedule Revenue assigns based on your expected withholding volume.

3. Register for SUI with the DES

Register with the Division of Employment Security (DES), part of the Missouri Department of Labor and Industrial Relations. New employers pay 2.376% in 2026 (1% for nonprofits) on a taxable wage base of $9,000 per employee. This tax is fully employer-paid.

The wage base can move up or down by a set amount each year depending on the Unemployment Compensation Trust Fund balance, so check the current figure at registration rather than relying on last year's number. After a couple of years of history, your rate becomes experience-rated.

4. Collect Employee Paperwork

Before anyone's first shift, collect three documents:

• Form I-9, verifying work eligibility, with Section 2 completed within three business days of the start date.
• Federal Form W-4, for federal withholding.
• Form MO W-4, the Missouri Employee's Withholding Certificate. It isn't valid unless signed, and a new one is required annually to keep any exemption in place.

Report the new hire through the Missouri New Hire reporting system within 20 days of the start date, counting calendar days. Most payroll software submits this automatically once the hire is entered into the system.

5. Set a Semimonthly Pay Schedule

Missouri law requires corporations doing business in the state to pay employees at least semimonthly, within 16 days of the close of each pay period. Executive, administrative, and professional employees, along with salespeople paid wholly or partly on commission, can be paid monthly instead if the employer chooses that option.

You're also required to give employees a statement showing total deductions at least once a month, separate from the paycheck itself. Building that into your payroll software from day one saves a manual step later.

6. Run Payroll and Make Deposits

Each pay period, calculate gross wages, apply federal withholding from the W-4, apply Missouri withholding from the MO W-4, and withhold the employee's share of Social Security and Medicare. You owe a matching FICA amount as the employer, along with federal and state unemployment tax.

Federal deposits follow the IRS's semiweekly or monthly schedule and get reported quarterly on Form 941. State withholding deposits follow the schedule Revenue assigned at registration. Our paycheck calculator shows federal and Missouri withholding together, and the W-4 helper walks new hires through both forms before their first check.

7. Close Out the Year

W-2s are due to employees and the Social Security Administration by January 31. Missouri also expects an annual withholding reconciliation so the totals on your W-2s match what you deposited across the year. Getting this reconciliation done early in January, rather than waiting for a notice, keeps you ahead of the per-form penalties that build up for late W-2s.

Frequently Asked Questions

How do I set up payroll for the first time in Missouri?

Get a federal EIN from the IRS, register with the Missouri Department of Revenue for withholding, register with the Division of Employment Security for a SUI account, collect I-9, W-4, and MO W-4 paperwork from each employee, then set a semimonthly pay schedule and run your first payroll.

What state tax form replaces the W-4 in Missouri?

Missouri employees fill out Form MO W-4, the Employee's Withholding Certificate, alongside the federal W-4. It must be signed to be valid, and a new one is required each year an employee wants to keep an exemption.

How often do Missouri employers have to pay employees?

Corporations doing business in Missouri must pay wages at least semimonthly, within 16 days of the close of each pay period. Executive, administrative, professional, and commissioned employees may be paid monthly instead, at the employer's option.

When do new hires need to be reported in Missouri?

Missouri employers must report every new hire and rehired employee within 20 days of the start date, counting calendar days including weekends and holidays.