the md5 utility is somewhere on the OS, so you'll need to know if your server has md5sum or md5 and where to get it, then in PHP use exec(). I have Windows 8.1 on my other PC, but kind of lazy to go check if it has MD5, I think it doesn't, I think its a 3rd party thing on Windows.
On Macs md5 is reachable anywhere so there is no need for the full path to it, your server may need the full path, you'll need a bit of trial and error to find out. Try a few probes in PHP:
echo exec('whereis md5'); // or md5sum, or just try ...
echo exec('md5 path/to/somefile.css');
Actual anwser to your question is:
$checksum = exec('md5 -q /Users/edward/Desktop/example.css');
// -q is quite mode, only the checksum is returned, without it, you'll get:
// MD5 (/Users/edward/Desktop/example.css) = 5e7f4d0bfa9da0c1527086c373dfc15f
// ... ain't got time for dat!
// btw that flag stuff is described in the man pages
// man md5