The phpMyAdmin version is usually automatically upgraded when you run a cPanel update to a newer version. However, if you’re not quite ready to upgrade cPanel, you easily install a newer version of phpMyAdmin. Please be aware that future cPanel updates will overwrite your manual installation.
You will need to go to the phpMyAdmin download page and pick your version. This tutorial is specific to version 2.11, but should work for any:
cd /usr/local/cpanel/base/3rdparty
mv phpMyAdmin hold_phpmyadminwget http://prdownloads.sourceforge.net/phpmyadmin/phpMyAdmin-2.11.2.2-english.tar.gz?download
tar -xvzf phpMyAdmin-2.11.2.2-english.tar.gz
mv phpMyAdmin-2.11.2.2-english phpMyAdmin
cp hold_phpmyadmin/config.inc.php phpMyAdmin/
chown -R cpanel:cpanel phpMyAdmin
Then load up phpMyAdmin from cPanel or WHM and you should see the new version