Why is the spelling of rhythm so exceptional?

Rhythm has a very unusual spelling, breaking a lot of the common rules of thumb for spelling words. The rh is unusual; the use of y as a vowel in the middle of the word is unusual; and the lack of a normal vowel between the th and the m is extremely unusual

What is its etymology, and why does it have such an unexpected spelling?

Solution 1:

Direct from Greek ῥυθμός (rhythmos). "rh" is not an unusual word start in Greek, "y" is just a vowel, "-os" turned into "-us" in Latin then fell off when accepted into English, so the vowel that would have been in the syllable with "m" went away.