LetsEncrypt is a FreeSSL provider. To enable LetsEncrypt on Cpanel Dedicated Server, login to SSH as user root and run

/scripts/install_lets_encrypt_autossl_provider

Next login to WHM as user root, go to Home > SSL/TLS > Manage AutoSSL and select “Let’s Encrypt™” as your Auto SSL provider.

Go to Options and select the check box “Allow AutoSSL to replace invalid or expiring non-AutoSSL certificates.”

See LetsEncrypt