If you install PHP as a CGI program instead of as an Apache or ISAPI module, then PHP scripts can be run from the command line just like any other shell script.
This is easier to do in a Unix setting, I believe.
Also, in a Unix setting, you can just use a couple of command-line browsers or browser-emulation tools to run web-based scripts. Lynx is the de facto standard Unix command-line browser, but "wget" (simple) and "curl" (more complex)are a couple of very interesting utilities for "pretending" to be a web browser while really downloading files or running web-based commands.
For your situation, for example, if you are using Unix you could create a bash script, that calls Lynx and tells it to go to a certain PHP page and then do nothing with the results, since it is the PHP page that you actually want to do something. This bash script could be run regularly as a cron job.