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