How Do I Set Up Payroll for the First Time? The Employer’s Complete Guide

Gusto Editors

There’s something we’ve got to tell you: You rock. You’ve started your business, and now you’re at the point where you’re ready to hire a few new employees and set up payroll.

It’s a big milestone for you — and you’ve created a job for someone else. How cool is that?

As exciting as growing can be, it comes with a new set of challenges. Terms like “business structure” and “EIN” are entering your vocabulary, and you’re probably starting to encounter a few confusing emotions that are the polar opposites of the elation you’ve felt so far.

We get it; we’ve helped thousands of business owners through rites of passage like setting up payroll for the first time.

We’ve broken down the steps into two parts: what to do before setting up payroll, and how to kick-start the process. Here’s our best advice for meeting most of the regulatory requirements for running payroll while saving yourself time and protecting yourself from IRS penalties.

Here’s what you’ll need to take care of before setting up payroll

Steps 1–4 are all about preparing information before you can actually tackle payroll. Fortunately, you’ll complete most of these steps just once. Take a few days to gather the following details and register for the appropriate accounts:

Step 1: Get an EIN

Before you can hire anyone, you need to get an EIN (Employer Identification Number) from the IRS. In case the terminology gets confusing, people also often refer to EINs as an “Employer Tax ID.”

You’ll use your EIN to report taxes and other info to the IRS and state agencies.

Apply for an EIN online and boom — your first task is in the bag.

Step 2: Get a local or state business ID (if necessary)

Some state and local governments require companies to have ID numbers for tax processing. Contact your local and state government officials to find out if you need an additional tax ID number.

We know it’s a little annoying, but once you’re done, you can proudly check that one off the list.

Step 3: Nail down your team’s info

Now that you’re becoming an employer, you’re going to be responsible for filing reports and taxes on behalf of your team. These are the details (and forms) you’ll need to keep on hand for each employee or contractor you hire:

  • Full name
  • Employment start or termination date
  • Tax filing number (Social Security number or EIN)
  • Date of birth
  • Current address
  • Compensation details: Make sure you take the step of putting details about compensation in writing to prevent disagreements from popping up.
  • Form I-9 to verify employees’ eligibility for employment in the US
  • A W-4 for employees (or a W-9 for independent contractors)

Keep in mind that gathering this info is just the first step. To stay compliant you’ll also need to do things like submit your employees’ I-9 form for verification.

Here’s the full list (and all the links you need) to stay compliant on your employee’s first day.

But we’re talking about setting up payroll here, so let’s keep the focus on what you need to do to get your employees paid (and keep them happy).

Step 4: Classify your employees

Before you even think about adding up the payroll numbers, you need to figure out who’s an independent contractor and who’s a full-time or part-time employee. Even if this seems obvious, there are legal definitions of each — and differences between the two — that impact how much you actually owe them and how you withhold their taxes. If it’s unclear, the IRS will help figure it out for you if you fill out Form SS-8.

Why is it so important to classify employees correctly? Well, if you accidentally classify an employee as an independent contractor, for example, you wouldn’t withhold income taxes for them or pay any payroll taxes. That means you could get stuck paying back payroll taxes as a result of your mistake.

Not to mention, you could have to amend your taxes and potentially pay interest or penalties. According to an Economic Policy Institute report, studies of multiple states have shown that 10 to 20 percent of employers misclassify their employees as independent contractors. Since employees typically cost companies 25 to 30 percent more than contractors do, you want to be sure you get it right.

Similarly, the FLSA makes distinctions between exempt and nonexempt employees—in other words, those who aren’t eligible for things like overtime and those who are.

Now you’re ready to dig in

Congratulations! You’ve got all the information you’ll need to set up your payroll. Steps 5–7 will take you through the rest of the process.

Step 5: Choose a pay period

Payday’s going to be a day your employees cherish, but what day should it actually be? And how often should you have it?

There are three things you need to think about to choose the right payroll schedule:

  1. What’s required by your state? Check out this list of federal and state payroll resources to see if there are any constraints about when or how you can run payroll.
  2. When is it best for you? Payroll is the largest expense for a lot of small businesses. Will running payroll cause cash flow problems? Is there a period of time when it’s more convenient for you to run it? Before your employees pass Go and collect $200, set up your schedule in a way you’re comfortable with.
  3. What do your employees need? Don’t forget that payroll is all about taking care of your team. They basically give you their labor on credit, and it can be hard for them if they have to wait a month to get paid. Try to get a sense of their needs and what they prefer — especially if they’re likely to have cash-flow issues of their own.

Once you decide what your pay period will be, be sure to let your employees know so they can plan accordingly.

Step 6: Pick a payroll system

Will you use a pad and pencil? Or will an online service make more sense?

The business of actually calculating payroll can be a little tough, and small business owners spend between one and five hours a month trying to get it right.

You’ll want to research your options and make sure you set up a payroll method that will help you save time and enable you to get all the nitty-gritty details right. A payroll provider should be easy to use and made to grow with your business. Of course, the payroll provider should also fit within your budget. 

When choosing the right payroll company, ask other entrepreneurs what they use and recommend, look at reviews online, and decide whether you want to handle payroll in-house or outsource it. Here are some questions to consider when you’re checking out your options:

  • Is it easy to use? Payroll can be complicated, so you’ll want to be sure the payroll provider leads you through a seamless process. Here are a few signs you’ll have a smooth user experience: The platform works well on mobile devices, has an intuitive menu structure, and contains easy-to-read text, clearly labeled buttons, and appealing colors.
  • Could I use it myself? Even if you plan to hire a bookkeeper, you should be able to use most of the features yourself. Ask the provider if it has a demo of the software, and navigate the service on your own. Do you understand the terminology? Do the features apply to your business? Does the provider offer a live-chat function and other help features?  
  • Can it grow with my business? Make a list of your current and future payroll needs, and check whether the provider meets them.

Step 7: It’s go time

Once you have your act together and decided on things like pay periods, you can actually start paying people. We hope some of that excitement you feel about your business is creeping back in.

It’s also a good time to share important details about the payroll process with employees. Like, when they can expect to be paid, how they’ll be paid (such as written check versus direct deposit), and any deductions they should know about. Add these details to your employee handbook.

Remember, though, that cutting a few paychecks isn’t the end of the road. If you only want to know the basics of what you need, you can stop reading right now. If you want to know what you’ll need to do once you’ve set up payroll for the first time, read on.

Ongoing payroll best practices

Process payroll on time, every time

Be on time with payroll each pay period. It keeps employees happy and keeps you from making mistakes like overpaying employees (or worse, underpaying them) because you’ve rushed through payroll.

Note also that many states have requirements about how soon you need to provide the final paycheck to a departing employee, so it’s good to be in the habit of sticking to a regular payday every month.

File payroll taxes on time

Be sure to meet the IRS deadline for payroll taxes, so you don’t get fined the IRS’s 10% Failure to Deposit Penalty.

You’ll need to pay city and state payroll taxes on time throughout the year, too, or risk getting hundreds or even thousands of dollars in additional fines from local tax agencies. And depending on the state, you may need to apply for a state unemployment insurance account. 

Here’s a quick table you can use to track the major deposit and filing deadlines through the year:

Tax When to depositFile this formDeadline to file
Social Security, Medicare, and federal income taxMonthly or semiweeklyForm 941Quarterly:April 30July 31October 31January 31
State and local income taxVariesVariesVaries
Federal unemployment tax (FUTA)Quarterly:April 30July 31October 31January 31Form 940January 31
State unemployment tax/insuranceVariesVariesVaries

Be meticulous and fill out forms correctly

Before you submit your payroll taxes, make sure you line up all those columns and lines, then triple-check to make sure each line item corresponds to your financial statement and payroll reports. Mistakes mean doing it all over again, which can cost a lot of time and money in the future.

Maintain squeaky-clean payroll records

Each time you run payroll, you’ll have to withhold federal income tax, Medicare, and Social Security from your employees’ pay. Each quarter, you’ll need to file Form 941, also known as the Employer’s Quarterly Federal Tax Return, to report how much you withheld (along with state-specific withholding forms).

Organize and find a secure place to keep up to four years of I-9 forms, W-2s, W-4s, state new hire forms, and copies of all your filed tax forms (Form 941, Form 940, and state tax forms). You’ll also need to maintain the dates and amounts of all tax deposits, timesheets, and pay stubs.

Keep everything on file for all active employees, and keep those files around for at least three years after an employee is terminated. Check with your state labor office and double-check federal laws to make sure you’re keeping track of everything that’s required.

This step can make it easier to spot issues before they arise, and it can help audits go smoothly (should they ever arise).

Keep these payroll checklists handy

There’s a lot to keep track of when it comes to running payroll, from finding the tax forms you need to remembering important dates and more. It’s easy to miss a form or two — or three — so we’ve set up a few quick checklists to help you keep all those details straight.

Your payroll squad

Payroll is complicated! That’s why it’s usually a team effort. Here’s who you might need to get involved in your payroll process:

  • Your payroll provider
  • An accountant or other financial professional 
  • A human resources business partner

Once you assemble your payroll squad, it’s time to divide and conquer. Each person will handle their piece of the payroll process and get together when needed. If your business is small and doesn’t yet have a finance or HR team, no problem. Just be sure you decide who will be responsible for regularly entering payroll numbers and approving payroll. 


You’ll need to fill out and submit various tax forms for payroll. We’ve gathered them into a list here:

Setting up a Gusto account

If you decide to partner with Gusto to run payroll, gather these details before setting up your account: 

  • Addresses: This includes the physical address where any employees work in the U.S., including remote employees. 
  • Employee information: You’ll need the name, hire date, manager, work address, employee email address, and compensation information for each employee. If you don’t have some of these details on hand, you can invite employees to enter their own information. 
  • Federal tax information: This includes your business’s federal EIN, company type, and legal entity name.
  • State tax information: You’ll need registration and compliance information for every state where employees work. 
  • Bank details: We’ll also need the routing number and account number for your business checking account. 
  • Pay schedule: We’ll need details about your company’s pay period, such as the first pay date and the days covered within each pay cycle. 
  • Payroll history: This includes information about the previous year’s payroll, so we can accurately calculate and report taxes. You can skip this step if you’re setting up your first payroll.
  • Signatory details: Who should sign the paychecks? We’ll need the signatory’s name, title, Social Security number, birthdate, phone number, and home address. 

It may be kind of a lot to absorb, but the good news is that you only have to set up payroll once. After that first time, you should get into a routine of handling your weekly and monthly payroll responsibilities, and then preparing quarterly and year-end tax filing and reporting. But it gets easier with time.

And pretty soon, you’ll be blown away by how much you rock (and roll) with payroll.

Looking for cost-effective payroll solutions for your business? Dive into our guide for expert recommendations and find affordable software that meets your needs.

Gusto Editors Gusto Editors, contributing authors on Gusto, provide actionable tips and expert advice on HR and payroll for successful business management.
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