Perl scripts need to be executable in order to run them on the server. You can do this using the FTP software you use to upload your files. Upload the files in the usual way, then perform the following on the uploaded file:

In WS_FTP: right click on the file and choose "FTP commands" then "SITE". Type in: 
chmod 755 filename.pl
and press "OK".

In CuteFTP: right click on the file > choose "Change File Attributes". In the manual section type:
755 and press "OK".

In Fetch: click on the file > choose Remote > Set Permissions. For 'Owner' tick all of the three boxes, for 'Everyone' tick "Read" and "Search/Execute" and press "OK". 

In Anarchie: click on the file > choose FTP > Send FTP Command > type in site chmod 755 filename.pl
and press "OK".