I'm a bit late but since everyone else seems to be wrong I'll hop in.
Baka janai バカじゃない literally means "you are not stupid." But translating it like that would be a stupid thing to do.
First off, baka バカ means "stupid". Ok.
desu です means "is", and dewanai / janai is the negative of desu, meaning "is not".
But here is the thing, when someone says baka janai they could be stating a fact "you are not stupid"
or they could be asking a question "baka janai ka?" or "baka janai no?"
in the latter, you'd be asking if someone is NOT stupid. Confirming if he is not stupid.
It's like saying "are you sure you aren't stupid?" Like if a vegetarian ordered meat you'd ask "aren't you a vegetarian?"
So that's where the nai in baka janai comes from.