Rafe Khatchadorian is the main protagonist of the Middle School series and is a student who has attended Hills Village Middle School, Cathedral School for the Arts, and Airbrook Arts. He is an artist, and imagines school as a prison for sixth, seventh and eighth graders. Rafe has come up with several missions for himself in an attempt to make life more interesting, though executing the operations seems to only land himself in hot water with authority figures. The operations he (and Leo) have come up with so far are as follows:
- Operation R.A.F.E., which stands for Rules Aren't For Everyone, in which Rafe attempted to break every single rule in the Hills Village Middle School Code of Conduct
-Operation Get A Life, over the course of which Rafe tries as many new things as possible without getting into too much trouble
-Operation Smoke Out the Bullies, during which Rafe worked with the other guys in his cabin to try to put a stop to the bullying done by the members of the Bobcat Alley cabin
-Operation S.A.M., which stands for Secret Artist Man, in which Rafe placed his own renditions of famous works of art around Hills Village Middle School, before changing the focus of the operation to be a PSA against bullying
His mother is Jules Khatchadorian, and his (adopted) sister is Georgia Khatchadorian. He has a deceased twin named Leonardo, who is known for most of the series as Rafe's imaginary friend. Rafe's father, Luca Khatchadorian, was a war hero who died before the events of the series. His maternal grandmother is known as Grandma Dotty, and has been living with them since the events of Book 2. Bear almost became Rafe's stepfather until he (Bear) nearly injured Jules in a rage and was subsequently kicked out of the house.
Rafe is currently friends with a boy named Flip, and was friends with Matty until they had a falling out. He also considers his English/Art teacher Ruthless Donatello a friend, as she is the only teacher to ever believe in his talents. He is also friends with Jeanne Galleta, although their relationship is somewhat stifled due to Rafe having a crush on her. He had his first kiss with Marley Grote, but in Rafe's own words, he's 'not sure where the whole "Rafe and Marley" thing is going'. For the time being, they seem to at least be more than just friends.
Rafe has shaggy black hair that probably matches his father's, since his mother has blonde hair. Rafe is an artist, who often draws his fantasies about the jail he calls school. His is almost always seen wearing a red shirt with a black stripe across it, and blue jeans with red sneakers. His other clothes include his ninja suit, the jail clothes he wore, his knight outfit, and his normal outfit, with a white shirt instead of a red one.
- Like Leo and Georgia, he was named after an artist, Raphael Sanzio da Urbino.
- Though he has gone on record as hating reading, Rafe has read The Book Thief (to antagonize Georgia by spoiling the ending), Holes, and has at least made an attempt at The Lord of the Rings: The Fellowship of the Ring.
- Rafe's favorite drink is Zoom, an energy drink he used to steal from Bear before he (Bear) moved out.
- He is a dreamer, seeing as he often illustrates his fantasies.
- He was put on house arrest for vandalizing the school.
- He hates school.