The Github Pro Documentation Page
People with write permissions for a repository can add a theme to a GitHub Pages site using Jekyll.
Changes to your site are published automatically when the changes are merged into your site’s publishing source. If you want to preview your changes first, you can make the changes locally instead of on GitHub. Then, test your site locally.
The theme chooser adds a Jekyll theme to your repository!
How the theme chooser works depends on whether your repository is public or private.
If you manually added a Jekyll theme to your repository in the past, those files may be applied even after you use the theme chooser. To avoid conflicts, remove all manually added theme folders and files before using the theme chooser.
To add a custom theme you will need to create your own theme using the jeykll theme edditor You can find more info, Here
Enter the config.yml file and create a new line and make it theme: and then enter the name of the theme you want/created. Ex: theme: minimal