Murphy revamped the Teenage Mutant Ninja Turtles Adventures title for Archie comics beginning with issue number five and created the characters Jagwar, Nova Posse, Snake-Eyes and Sarnath.

Stephen Murphy has been a staff writer on the 2003 TMNT animated series. He has also written many children's books for the new series, and recently worked on Fast Forward. Murphy wrote the majority of his work on TMNT Adventures under the name "Dean Clarrain". Stephen Murphy Blog

Murphy also created the comic book series The Puma Blues and Umbra, the latter was nominated for a Harvey award in 2007.

Murphy was a participant in the drafting of the Creator's Bill of Rights.