As you probably realize, this is almost certainly just an Apache config issue. Maybe this could have been tagged as OT for clarity.

Anyway, without details, I'll take a wild guess and say that you need to run a2enmod cgi (as root/sudo) and possibly check that your script is either in a configured CGI folder or has a configured CGI suffix.

Of course, that was just a guess but a bit more than RTFM ... which is probably a better solution.