cPanel 11.42 and higher supports MySQL 5.6. Upgrading is simple, and if you’re coming from MySQL 5.5 you will not need to recompile PHP after the upgrade.
If you’re coming from a version prior to 5.5, it’s recommended that you upgrade to 5.5 first, then to 5.6. The following upgrade process can be used for essentially any supported MySQL upgrade in cPanel versions 11.36 and higher.
First, set the cpanel.config file to the intended version:
/var/cpanel/cpanel.config
Look for mysql-version=, and set this to 5.6.
Then run the following script:
/usr/local/cpanel/scripts/check_cpanel_rpms –fix
This will remove the old MySQL version, install the new one, and update all tables.
If you are coming from a version earlier than 5.5, you will likely need to reinstall PHP by running EasyApache. This is due to the fact that PHP is compiled against the MySQL client libraries, which will be different after the MySQL is upgraded.
cPanel Server Management 