Make sure there is at least one file in it (even just the README.md)
ssh-keygen -t rsa -b 4096 -C "your_email@example.com"
GNU/Linux (requires the xclip package):
xclip -sel clip < ~/.ssh/id_rsa.pub
Copy the contents of the to your SSH keys to your GitHub account settings (https://github.com/settings/keys).
ssh -T git@github.com
Follow the instructions of repository to add a new remote
git remote set-url origin git@github.com:username/your-repository.git
Add the key to the ssh-agent
ssh-add ~/.ssh/id_rsa