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1099 E-Filing Module Overview

Eric Updated by Eric

This guide will walk you through e-filing 1099's.

Who must e-file

For e-filing threshold requirements, see IRS seeks to lower e-filing threshold.

Getting Started

1099s can be E-Filed with Payroll System's E-File add-on.

The annual release of the CFS W2/1099 E-File Add-On is around mid-December.

The IRS FIRE System typically is not in operation for 1099 e-filing from about early December to early January.
There is no need to file federal Form 1096 if filing 1099's electronically.
If you file electronically DO NOT send paper copies. This will result in a duplicate filing.

Want to use the new IRS portal for e-filing 1099's? See Can 1099s be filed with IRIS (Information Returns Intake System)?

1099 E-Filing Requirements

  • Have you applied for and received your TCC Code? If not, you'll need to submit an Online IR Application via the IRS eServices account.
    If you do not already have your TCC, it can be a lengthy application process. See Applying for a FIRE TCC.
  • Have you created an account on the IRS FIRE System?
  • Have you purchased the CFS W2/1099 program AND the W2/1099 E-File add-on?
  • Have you prepared the 1099’s that you desire to e-file? Check for missing or incorrect information on each 1099, such as employee’s SSN, name, address, city, state, and zip code. Also verify the accuracy of all wage data.
    Be sure to enter any required state income and withholding if it is required by your state.
    Payroll System 2021 does NOT support the Combined Federal/State Filing Program. You may be required to submit a separate file to your state.

Filing Corrections

See 1099 E-Filing: Filing Corrections.

Opening the 1099 E-File Module

Upon opening Payroll System, you will see the following window:

  1. As shown by arrows above, first Select e-file/MagMedia from the drop down menu.
    If the program displays a pop-up that you are not licensed for that portion of the program, do the following:
    a) Ensure you have purchased the e-file add on (this is sold separately from Payroll System), and
    b) Input the license code from that purchase.
  2. Double-click on Create 1098/1099/W-2G e-file/MagMedia Files.
  3. The e-file 1099 Create IRS File dialog will appear.
    If instead a dialog appears that the portion of the program is not yet released, either:
    a) wait until its release date (typically in December), or
    b) update the program.

Note the tabs for Steps 1 through Step 6 across the top.  Simply click on a tab to access a specific step.

  • The yellow box in the lower left-hand corner is field-specific help for the selected field (in this example, Transmitter Control Code).
  • The white box in the lower-right hand corner is instructions for the entire Step.

Step-by-step procedure

View CFS Instructional Video How to eFile 1099s

  1. See Step 1: Inputting Transmitter Data.
  2. See Step 2: Create IRS file.
  3. See Step 3: IRS Submittal.
  4. See Step 4: Create state file.
  5. See Step 5: State Submittal.

Further Assistance

Contact the IRS/ECC Information Reporting Program Customer Service Section (IRP/CSS).

  • Toll-free 1-866-455-7438
  • Monday through Friday from 8:30 am to 4:30 pm EST
  • or email

How did we do?

1099 E-Filing Step 1: Inputting Transmitter Data