Configure SSH remote git repositories with Connect to Git Repository wizard as you would with any remote git repository.

  1. Go to Administration > Add-ons. (For JIRA 7, go to Administration > Applications)
  2. On the sidebar, under Git Integration Plugin for JIRA section, select Git Repositories.
  3. Click Connect to Git Repository. The Connect to Git Repository wizard appears.
  4. Enter Repository location of your SSH git server. Click Next.
  5. Upload the private key or paste it on the provided field. Click Next.
  6. Enter Passphrase (if required). Click Next.
  7. The wizard will start cloning the selected repository. When the process is complete, the Permissions dialog is displayed.
  8. Click Next.
  9. Click Finish to complete the setup. The repository is added to the repositories list.

Here's a video to guide you step-by-step as stated above: