That sentence is perfectly fine. It means you attend the same school. Again, as I answered the other day, I strongly prefer the usage of 'at' as the preposition.

"We're in the same school." / "We got to the same school." 'at' refers to location. "Where are you?" - "at school."

I agree with Paul. 'We're at the same school' is perfectly fine and absolutely natural. That is exactly what most native speakers would say. Using 'in' in this sentence sounds awkward.

You can say "at" or "in" When you say "in" it pretty much meaning your in that precise location. Eg I'm in my room. And when you say at it usually means your doing something at that location. For example I'm at the store buying food. I'm at the store "it can mean that I'm outside the store"

You say we're in the same school...same class..same locality.