Learn Croatian: Ona je doma.

Actually, no! Je is a clitic (a short, unstressed word), and there is a strict rule that a clitic cannot be the very first word in a sentence. If you want to drop the pronoun ona (she), you have to swap the word order and say Doma je so that je takes the second spot.

If I include the pronoun, could I change the order to Ona doma je?

No, because of that same rule! The short verb je must sit in the second position of the sentence. In Ona je doma, Ona is the first word, so je steps right into that mandatory second spot.

Does je only mean 'is' for females?

No, je is the verb 'is' for any third-person singular subject. You will use it for on (he), ona (she), and ono (it), or when talking about a specific person, like in Marko je doma.

I learned that kuća means house. Why does this sentence use doma?

Kuća is a noun meaning the physical building of a house. Doma is an adverb that means the state of being 'at home'. When you are talking about someone's current location being their home, you use doma.