This problem may be caused by a custom (a self-signed) certificate. Make sure to install the latest JRE and then change the JAVA_HOME of JIRA server.

The above solution should work, otherwise, see below for the steps to workaround this issue:

1. From your JIRA Server, clone the repository manually using the git client.
cd /jira/home
cd data/git-plugin
git clone --mirror https://my-self-signed-repo/project.git

2. Make sure the JIRA user has access to the folder above.
3. Configure the repository to disable verification of the SSL certificate.

cd project.git
git config http.sslVerify false

Run git config http.sslVerify false in the repository folder.

4. Add repository to the Git Integration Plugin using Advanced setup.
5. Set repository root to the folder that was used in step 1.

The clone will be kept up-to-date and the SSL verification issues will be ignored.

There are alternative solutions to make Java trust this cert. Refer to the good articles from Atlassian which focuses on helping to resolve SSL Verification Issues:

  1. Unable to Connect to SSL Services due to PKIX Path Building Failed
  2. Connecting to SSL services

If the problem persists, please send us a support zip to give us a better view of the issue.