How to Connect a Private GitHub Repo to cPanel (Step-by-Step)

Deploying from GitHub to cPanel can feel tricky at first, especially with SSH keys and private repositories. This guide walks through a clean setup from scratch.

Why use this method?

Easy to update after each push
Works with private GitHub repos
More secure than manual uploads

Prerequisites

A cPanel account with Terminal/SSH access
A GitHub repository
Domain already pointed to your hosting account

1. Generate an SSH key on your cPanel server

In cPanel Terminal:

ssh-keygen -t ed25519 -C "cpanel-deploy" -f ~/.ssh/id_ed25519 -N ""
cat ~/.ssh/id_ed25519.pub

Copy the public key output.

2. Add the key to GitHub

In your GitHub repo:

Go to Settings → Deploy keys
Click Add deploy key
Paste the public key
Keep write access off unless you specifically need push from server

This allows your server to read your private repo securely.

3. Configure SSH on cPanel

Create/update ~/.ssh/config:

Host github.com
  HostName github.com
  User git
  IdentityFile ~/.ssh/id_ed25519
  IdentitiesOnly yes

Then run:

chmod 600 ~/.ssh/config
ssh -T git@github.com

4. Clone the repository using SSH

Use SSH URL (not HTTPS):

cd ~
git clone git@github.com:YOUR_USERNAME/YOUR_REPO.git repositories/your-repo

5. Deploy files to your website folder

Copy repo files to your domain’s document root (example: public_html):

rsync -av --delete ~/repositories/your-repo/ ~/public_html/

Now your site files are live.

6. Updating after future GitHub pushes

When you push new changes:

cd ~/repositories/your-repo
git pull origin main
rsync -av --delete ./ ~/public_html/

Common errors and fixes

could not read Username for ‘https://github.com’
You used HTTPS. Switch remote to SSH.
Permission denied (publickey)
Wrong/missing deploy key, or SSH config not using correct key.
Wrong branch (main vs master)
Pull the branch that actually exists.

This setup gives you a secure and repeatable GitHub-to-cPanel deployment flow without making your repository public.