I'm assuming FMS 10 here...
If your script is server compatible, you can simply set server's scheduler to run the script.
If it's not, you can set up a robot file to log in as a client and run it for you.
To check server side compatibility, open the script and select "Server" from the show compatibility drop down. Be aware that some script steps such as Import Records will show as "compatible" but are severely limited in what they can actually do when run from a server schedule.
To set up a filemaker Robot file, create a new empty database file.
Give it a script:
Perform Script [//select the report script you want to run in the hosted file]
Now specify scheduler to open the robot file at a specified time.