You'll probably need to contact the server's admin/tech support. You can't do this yourself if they haven't provided an interface. You can check your server's tech support FAQ/features to see if you have this interface.
You'll them what filename you want them to run...say 'mycronscript.php'. Once they've set up a cron job to run that script, you can upload new versions with new functionality via FTP, provided you don't change the directory/name.
(In other words cron finds the scriptname and runs it, it doesn't run some cached code that you can't get to.)
There are some challenges with getting cron to work with PHP. For example you'll need to use absolute pathnames in includes. Call back if you need help.