1. Login to your Cpanel and go to Cron jobs.
2. Select Standard and enter (no quotes) "/usr/bin/php -q /home/USERNAME/public_html/PathToFile" into the Command field. USERNAME is your Cpanel username.
3. You will also need to setup the times for this to run.
Example:
My username is "domdom". The PHP file I want to run resides in /phpfiles/mycron.php. The command to run it via the Cron Manager will look like this:
/usr/bin/php -q /home/domdom/public_html/phpfiles/mycron.php