How To Integrate Jira With Payrun
Noah Parker23 Aug 2026
The Jira integration in Payrun connects selected Jira projects with existing Payrun projects. It lets you map corresponding users, statuses, and priorities, then sync project data between the two systems.
After the integration is connected, you can manage project mappings, control Auto sync, resync individual projects, edit mappings, stop an active sync, remove a project, or remove the complete Jira integration.
Before You Connect Jira
Before you start, make sure you:
Have access to Settings > Integration in Payrun.
Can sign in to the Atlassian account that contains the Jira projects you want to connect.
Have permission to authorize Payrun for the required Jira data.
Have the necessary projects already available in Payrun for mapping.
Know which Jira projects you want to connect with Payrun.
Your Payrun subscription can limit how many Jira projects you can map. Payrun displays the applicable project limit during setup.
How To Connect Jira To Payrun
To start the Jira integration:
Sign in to Payrun.
Go to Settings.
Select Integration.
Find Jira.
Click Connect.
Payrun redirects you to Atlassian to authorize the connection.
How To Sign In To Atlassian
Atlassian may ask you to sign in before you can authorize Payrun.
Enter the email address associated with your Atlassian account.
Click Continue.
Complete the required sign-in process.
Other sign-in methods may also appear depending on your Atlassian account.
If Atlassian displays an account that you do not want to connect, use the available option to sign in with another account.
Make sure you use an Atlassian account that has access to the Jira projects you need.
How To Authorize Payrun
After you sign in, Atlassian displays the permissions Payrun is requesting.
The authorization screen may include access to:
View Jira user information.
View Jira work data.
Update Jira work data.
Review the Jira site and requested permissions before you continue.
Click Accept to authorize Payrun. Select Cancel if you do not want to continue.
After authorization, Payrun takes you to the Jira project selection process.
How To Select Jira Projects
The Select projects to sync page displays the Jira projects available through the connected account.
Each project can also show its number of work items.
To select projects:
Review the available Jira projects.
Select the checkbox beside each project you want to connect.
Check that your selections are within your subscription limit.
Click Continue.
Only selected projects move to the mapping stage.
How To Map Jira Projects To Payrun
After project selection, Payrun opens the Map projects page.
Each selected Jira project appears in the Jira project column. You can associate it with an existing project in Payrun.
To map a project:
Find the Jira project you want to configure.
Open the Select project dropdown.
Choose the corresponding Payrun project.
Click Map.
Configure the relevant users, statuses, and priorities.
Save the mapping.
Repeat the process for your other selected projects.
Clicking Map opens the detailed mapping configuration for that Jira and Payrun project pair.
How To Configure Jira Mappings
The Configure Jira mappings page identifies the current project pair at the top:
Jira project → Payrun project
You can then configure corresponding values for:
Users
Statuses
Priorities
Map the values that need corresponding Payrun values for the project.
How To Map Jira Users
The User section lets you associate Jira users with Payrun users.
To map a user:
Find the Jira user on the left.
Open the corresponding Payrun user dropdown.
Select the appropriate Payrun user.
Repeat for other users you need to map.
Payrun displays a progress counter, such as 1 of 3 mapped, so you can see how many user mappings have been configured.
How To Map Jira Statuses
The Status section associates Jira workflow statuses with Payrun statuses.
To configure a status:
Find the Jira status.
Open Select a status under the Payrun status column.
Choose the corresponding Payrun status.
Repeat for the other statuses you need to map.
The available Jira statuses depend on the selected Jira project.
A counter at the top of the section shows your mapping progress.
How To Save A Project Mapping
After you configure the relevant users, statuses, and priorities:
Review the mapping.
Click Save & return.
Payrun returns you to the Map projects page.
The project status changes from Pending to Mapped after its mapping configuration has been saved successfully.
Repeat the process for your remaining selected projects.
Jira Integration And Project Statuses
Payrun uses several statuses throughout the Jira integration process.
Pending: The selected project's mapping setup has not been completed.
Mapped: The project's mapping configuration has been saved.
Connected: The Jira integration is connected to Payrun.
Active: The mapped Jira project is active in the integration.
Syncing: Payrun is currently synchronizing the project.
The available actions can change according to the project's current status.
How To Start Jira Sync
After you finish the necessary project mappings:
Return to the Map projects page.
Review your Jira-to-Payrun project mappings.
Check the mapping statuses.
Click Start sync.
Payrun displays a Syncing Jira data window while it processes the synchronization.
Successful Jira Sync
When synchronization succeeds, Payrun displays a Connected! message with a success indicator.
Click Continue.
The Jira integration is now connected.
When you return to Settings > Integration, the Jira card displays:
Status: Connected
Manage
Click Manage to access the connected integration and its project mappings.
Failed Jira Sync
If synchronization cannot be completed, Payrun displays:
Sync failed
The message asks you to try the Jira sync again.
Click Close and retry the sync. If the problem continues, confirm that your Jira connection and project mappings are still valid before trying again.
How To Manage The Jira Integration
To manage an existing Jira connection:
Go to Settings > Integration.
Find Jira.
Confirm that the status is Connected.
Click Manage.
The Manage Jira integration page provides access to your synchronization settings and project mappings.
For each mapped project, you can see:
Jira project
Payrun project
Work items
Status
Available actions
How Auto Sync Works
The Auto sync option controls automatic synchronization for the Jira integration.
When Auto sync is active, Payrun displays the setting as Enabled.
Use the toggle to enable or disable Auto sync based on your organization's synchronization requirements.
Auto Sync Vs Resync Project
Auto sync controls automatic synchronization for the Jira integration.
Resync project manually starts synchronization for a specific mapped Jira project when that action is available.
Use Resync project when you need to initiate synchronization for one project without changing the complete integration.
How To Manage A Jira Project
Each mapped Jira project has a three-dot menu under Actions.
Depending on the project's current state, the menu can include:
Edit mapping
Resync project
Stop sync
Remove project
Edit Mapping
Use Edit mapping when you need to change an existing Jira project configuration.
To access it:
Find the mapped project.
Click the three-dot menu.
Select Edit mapping.
Update the required mapping values.
Save your changes.
Resync Project
Use Resync project to manually start synchronization for an individual mapped project.
To resync:
Find the active project.
Click its three-dot menu.
Select Resync project.
Payrun starts synchronization for that project.
Stop Sync
When a project has the Syncing status, the Actions menu can provide a Stop sync option.
To use it:
Find the project currently marked Syncing.
Open its three-dot menu.
Select Stop sync.
Stopping the project sync does not remove the complete Jira integration.
Remove Project
Use Remove project when you no longer want an individual Jira project included in the integration.
To remove a project:
Open Manage Jira integration.
Find the project you want to remove.
Click the three-dot menu.
Select Remove project.
This action applies to the selected project rather than the entire Jira integration.
How To Remove The Jira Integration
To disconnect Jira completely:
Go to Settings > Integration.
Open the connected Jira integration.
Click Remove Integration.
Review the confirmation message.
Click Remove to confirm.
Click Cancel if you want to keep the Jira integration.
Payrun warns that removing the integration will stop synchronization of projects and tasks from Jira.
You can reconnect Jira later from Settings > Integration.
Common Jira Integration Issues
Why Does A Jira Project Show Pending?
A Pending status means the project's mapping setup has not been completed.
Select the corresponding Payrun project, click Map, configure the relevant mapping values, and save the configuration.
Why Can't I Start Jira Sync?
Check the mapping progress on the Map projects page.
Complete the necessary project mappings before you start synchronization.
Why Can't I Select More Jira Projects?
Your Payrun subscription can limit the number of Jira projects you can map.
Check the project limit displayed on the Select projects to sync page.
Why Don't My Jira Projects Appear?
Make sure you connected the correct Atlassian account and Jira site.
The connected Atlassian account needs access to the Jira projects you want to select.
What Should I Do If Jira Sync Fails?
Click Close on the failed sync message and try the synchronization again.
If the issue continues, check that the Jira connection and relevant project mappings are still valid.
Why Does A Project Show Syncing?
A Syncing status indicates that Payrun is currently processing synchronization for that project.
Open the project's Actions menu if you need to access the available synchronization controls.