MySQL and PHP upgrade on cPanel are very simple process, here is a list of steps that needs to be taken to upgrade these two components:

1. Login to your WHM as root.

2. Go to WHM >> Server Configuration >> Tweak Settings, scroll down to “MySQL” section, switch radio button to “5.0” and click “Save” at the bottom of the screen.

3. For this to take effect, open root level ssh session to your server and run the “/scripts/mysqlup” command, wait until installation will be completed.

4. Login to WHM as root.

5. Go to WHM >> Main >> Software >> Apache Update.

6. Click on the “Load Previous Config” button (if exists).

7. Select required PHP version and PHP options that your applications may need.

8. Click “Start build” button at the bottom of the screen and wait 15-30 minutes. (depend on the connection as well)

For MySQL upgrade, you may also need to run /scripts/perlinstaller –force Bundle::DBD::mysql.
Please note that updating from a previous version of MySQL® to a later version is not automatically reversable. You should backup your databases if you think you might wish to downgrade in the future.
For php/Mysql upgrade, kindly make sure that your applications are compatible with the latest version before do the upgrading.