USF coach Jim Leavitt made the announcement Tuesday.
"Wally did a great job for us, we will sorely miss him and his wife, Barbara," Leavitt said. "I am absolutely proud of everything he has done here and the success he has brought to USF. We wish him luck at Iowa State and I know that he will always be successful because of his tremendous character."
USF has been ranked in the top 30 in total defense in the Bowl Subdivision (Division I-A) in six of the past seven seasons -- including a No. 10 ranking in 2008 -- with Burnham in charge.
Burnham, 67, had worked for nine seasons at USF, including the past eight as defensive coordinator or co-defensive coordinator. He was promoted to associate head coach prior to the 2007 season.
Earlier in his career, Burnham served as defensive coordinator for five seasons at South Carolina on Brad Scott's coaching staff after nine seasons as Florida State's linebackers coach. The Seminoles claimed the national championship in 1993 during Burnham's final season coaching there.
The hiring fills a hole on the staff of new Iowa State coach Paul Rhoads, who had been looking for a defensive coordinator since his hiring on Dec. 23.
Burnham's announcement comes as Rhoads is looking to fill another position on his staff. Tight ends coach and recruiting coordinator Scott Fountain left the Cyclones' staff Tuesday to accept an administrative position on Gene Chizik's staff at Auburn.
Tim Griffin covers college football for ESPN.com. You may contact him at firstname.lastname@example.org.