Peterson's early works for Marvel include a New Warriors annual and a fill-in in X-Factor in 1992 The Unofficial Handbook of Marvel Comics Creators. Later in the year, he had a short run in Uncanny X-Men, drawing the title's issues of the "X-Cutioner's Song" crossover.

Peterson left Marvel to join Top Cow, pencilling the ongoing title Codename: Strykeforce. After the title's cancellation, he wrote and drew the creator-owned title Arcanum, before returning to Marvel in 1999 to work on several X-Men spinoff mini-series.

He left Marvel once more to become Art Director of CrossGen Comics The Brandon Peterson Gallery » About Brandon Peterson, but returned for another stint on Ultimate X-Men and the mini-series Ultimate Vision and Strange.