Had the same problem.
With SourceTree, do the following:
- Generate your Personal access tokens in Github account setting.
- Double click a repository in SourceTree, click
Settingicon in the top right of the popup window. - Click
Remotesin the menu tab. You will see the remote URL of this repository, which should be like thishttps://github.com/username/repo.git. - Click
Editand change it tohttps://<your_token>@github.com/username/repo.git.
DONE.