The move is a promotion for Emanuel, and a chance to return to a familiar place. He coached with the Boilmakers from 1997 to 2004, including time as an assistant head coach at Purdue.
"We are happy for Gary to have this opportunity to be a defensive coordinator at the Football Bowl Subdivision level,'' Rutgers coach Greg Schiano said. "We thank him and his wife, Angela, for their contributions to our program."
Emanuel was with Rutgers for two seasons, and was instrumental in recruiting Maryland for the Scarlet Knights. He and Purdue coach Danny Hope were assistants together under former Boilermakers head coach Joe Tiller.
"I am happy to be coming back to Purdue," Emanuel said. "The eight years I spent working with the Boilermaker program before were great. I'm excited to be working with Danny again, and I look forward to getting started with the players and coaches."
He is the third assistant to leave Rutgers this offseason, and each one left for a higher-ranking position.
Receivers coach Brian Jenkins left to become the head coach at Bethune-Cookman and was replaced by P.J. Fleck. Recruiting coordinator and tight ends coach Joe Susan was named the head coach at Bucknell last week. No replacement has been named yet for Susan.