Carlisle, 47, has been with the Trojans since Carroll took over in 2001. He was chosen as national collegiate strength and conditioning coach of the year in 2006 from the Professional Football Strength and Conditioning Coaches Society.
"I want people to know that I'm walking away, not running," Carlisle said in a statement released by USC. "There's not a reason for me to leave except that this is a great opportunity for me to continue my career and take a step in my evolution as a strength coach. ...
"Lane Kiffin and the USC administration wanted me to stay and I really appreciate that."
Jamie Yanchar, who has worked at USC since 1990, will be the Trojans' interim head strength and conditioning coach.