Longer answer: if you have the script set as set user ID root, you can run it as root. However, there may well be restrictions as to where the script must be located, what its other permissions must be, etc. And Perl may invoke taint checking when run setuid.

As far as cron, there are crontab entries for both the system (root) and individual users, at least on my Linux system (you don't say what kind of Unix system you have). If you're root, you can add crontab entries that will run as root.