Are the words philia (Greek) and filia (Latin) pronounced differently? And If so how?

Philia is pronounced FILL-ee-uh, whereas filia is pronounced FEE-lee-uh.

They’re more alike now in pronunciation than they would have been in classical times. The pronunciation of “ph” as our “f” only developed in the second century. Prior to that, both Latin and Greek pronounced it as an aspirated “p”.

There doesn’t appear to be an etymological connection.

In Attic Greek, “philía” (‘friendship’) would have been pronounced “pʰilí.a” (the accented “i” was most likely higher pitch rather than stress, but stress is how we read the accents most of the time). The little “h” next to the “p” represents the aspirated “p”, as @thorninmud mentioned, which is the “p” at the beginning of English words like “pat” and “ping”.

The Latin word “filia” (‘daughter’) would have been pronounced ”ˈfiː.li.a” with long “i” and stress on the first syllable. The two are not etymologically related, as far as I know. “Filia” comes from the Indo-European root meaning “suckle”. “Philia” comes from the Indo-European root meaning “harmony/friend”.

Essentially, the Greek word is “pee-LEE-ah” and the Latin word is “FEE-lee-ah”.

It has been my understanding that no one is actually sure of how one pronounced classical Greek or any of the other ancient dialects.

I wanted to say what @gailcalled said. Now all I say is that.

@gailcallled we can’t know with absolute certainty how Ancient Greek was pronounced, but we are reasonably certain about it, based on comparison with related languages.