Learn Russian: Кто вам звонил ночью?

вам is the Dative case of вы (you, formal or plural). In English you just call someone, but in Russian, the verb звонить (to call by phone) always requires the Dative case. Think of it as making a phone call to someone.

Why is the verb звонил in the masculine past tense? What if a woman called?

In Russian, the question word кто (who) is grammatically singular and masculine. Whenever кто is the subject of a sentence, the past tense verb must take the masculine singular form (звонил), even if you suspect a woman or a group of people made the call.

I learned that night is ночь. Why is it ночью here?

ночь is the basic dictionary word for night. To say at night or during the night, Russian changes the word into the Instrumental case, which gives us ночью. You can think of it acting as a time word here.

Could I change the word order and ask Кто звонил вам ночью?

Yes, you absolutely can! Russian word order is flexible, so both are grammatically correct. However, placing the short pronoun right before the verb (вам звонил) is the most natural-sounding and common way to structure this question.