Export Payroll Data to Paychex

The Paychex Payroll Export report lets you export approved timesheet data from ClickTime into a CSV file formatted for Paychex’s timesheet import. Once configured, it provides a repeatable way to move worked time, overtime, and time off from ClickTime into Paychex for payroll processing.

Who this is for: Administrators who run payroll and need to move approved time and time off from ClickTime into Paychex.

Requirements: You must be a ClickTime Administrator to run this report. You will also need your organization’s Paychex Company ID, the Paychex Pay Component for worked time (and overtime, if applicable), the values for each Leave Type you want to export, and each employee’s Paychex employee identifier.

Where to find it: Go to Company → Reports, then open the Accounting & Payroll Exports or Miscellaneous section and choose Paychex Payroll Export.

You can jump to a section:

• Before you begin: Configure Paychex values in ClickTime
• Set the Company ID and Pay Component for worked time
• Add Accounting Package IDs to Leave Types
• Add Accounting Package Person IDs to people
• Running the Paychex Payroll Export
• Columns in the Paychex export file

Before you begin: Configure Paychex values in ClickTime

Before you can run the Paychex Payroll Export, your ClickTime account must be configured with the Paychex values that identify your company, worked time, leave types, and employees:

• Paychex Company ID (Company custom field) — the Company ID associated with your organization’s Paychex account.
• Paychex Pay Component (Company custom field) — the Pay Component Paychex uses for regular worked time (and, if applicable, additional Pay Components for overtime, as defined in your Paychex account).
• Leave Type Accounting Package ID — codes that map each ClickTime Leave Type to a Paychex time-off or earning code.
• Accounting Package Person ID — the value that links each ClickTime person to the correct employee in Paychex (used as the Employee ID in the export, i.e., their Paychex Employee ID).

Once these are set up, you can generate Paychex-compatible payroll files for any approved timesheet period.

Company ID and Paychex Pay Component for worked time

The first step is to configure your Paychex Company ID and the Paychex Pay Component for worked time. These values are stored in Company-level Custom Fields in ClickTime.

Create the Paychex Company ID custom field

1. Go to Company → Preferences → Custom Fields.
   
2. Click Add Custom Field in the upper-right corner.
   
3. Set the following values (these are case-sensitive and must match exactly):
   • Custom Field Name: Paychex Company ID
   • Display Name: Paychex Company ID
   • Type: Text
   • Association: Company
4. Click Save.
   

Create the Paychex Pay Component custom field

Next, create a second Company-level custom field to store your Paychex Pay Component for worked time. This value should match the Pay Component used in Paychex to represent regular hours.

If your Paychex setup uses a different Pay Component for overtime, confirm that value with Paychex and ensure it is configured and used consistently when you import the export file.

1. From Company → Preferences → Custom Fields, click Add Custom Field again.
2. Set the following values (also case-sensitive):
   • Custom Field Name: Paychex Pay Component
   • Display Name: Paychex Pay Component
   • Type: Text
   • Association: Company
3. Click Save.
   

Important: For both custom fields above, the Custom Field Name and Display Name must match exactly (including capitalization) for the Paychex export to work correctly.

Enter your Company ID and Pay Component values

1. Go to Company → Preferences.
2. Scroll to the Custom Fields section. You will see the newly created Paychex Company ID and Paychex Pay Component fields.
3. Enter your organization’s Paychex Company ID and the Paychex Pay Component for worked time.
4. Click Save. 
   

Leave Type Accounting Package ID

The Paychex export uses each Leave Type’s Accounting Package ID to populate the Pay Component for time off rows. This value should correspond to the code for that time off type in your organization’s Paychex account.

We recommend configuring all active Leave Types you may export (Approval Required, Approval Not Required, Company Holidays, Externally Managed) so the report can run successfully for any approved timesheet period.

To configure Accounting Package IDs for Leave Types:

1. Go to Company → Preferences → Leave Types.
   
2. Find a Leave Type you plan to export and click the edit (pencil) icon.
3. In the Leave Type details, click Edit Section for Basic Information and locate the Accounting Package ID field.
4. Enter the value corresponding to the Paychex Pay Component or code for this time off type.
5. Click Update to save.
   

Repeat these steps for every Leave Type you want to include in the Paychex export.

Important: The export will fail if it encounters a time off entry for a Leave Type that does not have an Accounting Package ID, even if that Leave Type is inactive.

People Accounting Package ID

The Accounting Package Person ID on each person’s record is used as the Employee ID in the Paychex export. This should match the employee’s identifier in your Paychex account (their Paychex Employee ID).

If your account also uses ClickTime’s separate Employee Number field, note that the Paychex Payroll Export does not read that field — it only uses the value in Accounting Package Person ID.

To configure this for each person you plan to include in the export:

1. Go to Company → People and click the edit (pencil) icon for a person.
2. On the Person Details page, click Edit Section for Basic Information.
3. Scroll to the Accounting Package Person ID field and enter the employee’s Paychex employee identifier.
4. Click Update to save.
   

Make sure you enter this value for every person you plan to export. In the Paychex export file, this value appears in the Employee ID column.

Running the Paychex Payroll Export

Once your Company ID, Pay Component, Leave Types, and Accounting Package Person IDs are configured, you can generate the Paychex payroll export.

1. Go to Company → Reports.
2. Open the Accounting & Payroll Exports or Miscellaneous section and locate Paychex Payroll Export.
3. Click the report name, then click Run Report to open the report criteria page.
    

On the report criteria page, you can choose:

• The timesheet period to export.
• Which people, divisions, and employment types to include.

You will also see options to label exported entries, so you can avoid exporting the same approved timesheets more than once. For more information on labels, see Labels.

Important: This report only includes approved timesheet data. You can only run it for complete timesheet periods, and only data from approved timesheets in that period will be included. If you run it for dates that overlap part of a timesheet period, hours for the entire approved timesheet will be included.

Please note: this report may take up to 1 hour to finish processing.  Once the report run is triggered, it is processed in the background and an email will be sent when the report is ready for review (to the user who ran the report).  At that point, you can navigate back to Company >> Reports in ClickTime to download and review the report.

If the email you receives states there was an error processing the report, please reach out to ClickTime Support (support@clicktime.com).

Columns in the Paychex export file

Running the Paychex Payroll Export generates a CSV file in a format compatible with Paychex. The report aggregates all approved worked time, overtime, and time off for the people and timesheet period you selected. Each row represents one combination of employee + time type (worked, overtime, or a specific leave type).

The columns are:

• Column A – Company ID
  • Populated from the Paychex Company ID Company-level custom field.
• Column B – Employee ID
  • Populated from the Accounting Package Person ID field on the Person Details page.
• Column C – Pay Component
  • For worked time rows, this is your Paychex Pay Component (Company-level custom field for regular hours).
  • For overtime rows, this is the overtime Pay Component defined in Paychex.
  • For time off rows, this is the Accounting Package ID from the corresponding Leave Type.
• Column D – Hours
  • The number of hours corresponding to the type of time in that row (worked, overtime, or a specific leave type).

Once you’ve downloaded the CSV file, you can import it directly into Paychex. If you need to make manual changes, do not rename the column headers or change their order, as Paychex expects this specific layout.

Need help? For questions about importing the CSV into your organization’s Paychex account, please contact your Paychex support representative. For help configuring custom fields, Accounting Package IDs, or troubleshooting the export in ClickTime, please contact ClickTime Support.