I definitely remember this story, or at least one very similar. I don't remember brain transplants exactly, but other parts line up.
If it's the same story I'm thinking of, it was broken into six parts, and you generally read two parts read per year in elementary school (Grades 4 / 5 / 6). It was always the very last story in the "reader" (as they were called), a book of many short stories. I would have read it around 1996-1998.
I think it was called "Journey to the Stars" or "Journey through the Stars" or something like that, but so far my Googling hasn't revealed anything concrete. At least one of the readers was called "Star Heights" or something like that and had a bunch of musical instruments lined up to look like buildings.
Some other plot points I remember that might help your search:
1) The kids (six, if I recall correctly) are abducted at a science museum and sent into space via a strange orange-colored sphere.
2) They meet a race of friendly "blue people" who are three meters tall. The blue aliens have no idea where Earth is, or how to get the kids home, but give them a spaceship to help them try and find Earth.
3) They land on a planet based similar to Alice in Wonderland where there is a "Queen of Hearts" and the aliens on the world attack them due to stealing "tarts".
4) One of the kids (a girl) is deaf, and at first somewhat alienated from the other kids. But eventually her deafness helps them escape a predicament where they are trapped by a loud noise, and they come to accept her.
5) The ship takes them to a few different planets, eventually landing on a desolate planet destroyed by global warming, where they find an alien who tells them the blue alien's ship will not be able to get them back to Earth. But, he can send them back to Earth via the orange spheres that brought them to space in the first place.
5) They go back to Earth to find that nobody noticed they were gone because they were placed by look-a-like aliens (or possibly androids). I don't remember what happens after that.
I suspect it may be the same story asked about in this question:
Looking for a story about kids sent into space on an alien spaceship and are replaced by aliens who look like them
I hope some of that helps! If I find anything/think of anything else, I'll let you know.