1- Login to your cPanel account.
2- Find Let's Encrypt SSL.
3- Click on Let's Encrypt SSL.
4- Find the domain on which you want to install a Free SSL Certificate.
5- Click on the Issue button next to the domain name.
Please note that, don't change any settings here.
7- Click on the Issue button.
Free SSL Certificate will be installed at your domain.
Now how to repair/fix SSL warning showing in cPanel?
1- Click on the setting icon.
It will redirect you to SSL/TLS Status page.
2- Click on view certificate.
3- Now click on the button Autofill by Certificate button.
4- Then scroll down and click on the Install Certificate button.
SSL warning has successfully been fixed.