By the PayAdvisors team · Reviewed by Jessica Bautista, Tax & Benefits Manager
S Corp Payroll Setup After the Election: A Checklist
Six things have to exist before your first paycheck: the accepted election, the EIN, state accounts, the salary figure, a payroll system or team, and a calendar. Here they are in order.
A payroll team can take this list from step three onward.
You elected S corp, or you are about to. Here is what has to exist before the first paycheck, in the order it has to happen.
1. The election itself
Form 2553 is due no more than 2 months and 15 days after the start of the tax year it covers, or any time in the year before. It goes to the IRS by mail or fax.
The IRS usually answers within about 60 days. Keep the acceptance letter; your payroll team and your CPA will both ask for it.
Missed the window? Rev. Proc. 2013-30 offers relief where there was reasonable cause, if filed within 3 years and 75 days of the intended date. That is a conversation with your CPA.
2. Your EIN
Payroll runs under the company's EIN. If you formed the company recently or changed its form, confirm with your CPA which EIN the IRS has on file for it.
Keep the EIN assignment letter with the election acceptance. Together they are the two documents every account application asks for.
3. State payroll tax accounts
Before the first paycheck, most states need two accounts opened in the company's name: a withholding account and an unemployment insurance account. Some states add local or paid-leave registrations.
Timing runs from immediate to several weeks. Running payroll before the accounts exist is how first-year S corps collect agency notices.
4. The salary figure
Your CPA sets reasonable compensation. Payroll cannot start without the number, and the number should be written down with the reasoning behind it.
5. A payroll system, or a team
Someone has to calculate the withholding, move the deposits, file the returns and produce the W-2. The choice is a payroll account you run, or a payroll team that runs it for you.
Rather not run any of this yourself?
On the S corp payroll package, our team registers your state accounts, runs your monthly payroll, files every return and issues your W-2.
See S corp payroll Get started6. The calendar you are signing up for
- Tax deposits: monthly for most small employers, by the 15th of the following month
- Form 941: April 30, July 31, October 31 and January 31
- State withholding and unemployment returns: quarterly in most states, on their own dates
- Form 940: January 31
- W-2 to you and W-3 to the SSA: January 31
What to keep on file
The IRS letter accepting the S election
The EIN assignment letter
Your CPA's salary memo
State account numbers and their filing schedules
Each quarter's filed returns and deposit confirmations
Your W-2 and W-3 copies
Setup questions
How long does S corp payroll setup take?
The state accounts set the pace. Some states issue numbers right after online registration; others take weeks. Payroll setup itself is quick once the numbers exist.
Can I run payroll before my state accounts are open?
You can calculate it, but you cannot file or deposit correctly without the account numbers. Most agencies issue notices and penalties for that gap.
Do I need a payroll account if I am the only employee?
You need payroll. Whether you run it in your own account or a team runs it for you is the choice.
What if my election was filed late?
Rev. Proc. 2013-30 relief exists for late elections with reasonable cause. Your CPA handles that filing; payroll follows the accepted effective date.
Does PayAdvisors file Form 2553 or get my EIN?
No. You arrive with both. We register your state accounts, set up payroll and run it.
Related
See the S corp payroll package Read: S corp payroll with one employee, you See the payroll startup package
Talk to a payroll team about your S corp setup
Last reviewed October 20, 2026. General information, not tax or legal advice for your situation.
Next step
Start from step three with a team
Book a call with your EIN letter, your election acceptance and your CPA's salary figure in hand.
We register the accounts, set up payroll and run it, in all 50 states.
Call us Monday through Friday.