Assistant coach Isaac Brown will serve as the program's interim bench boss.
As part of the terms of Marshall's resignation, Wichita State's Intercollegiate Athletic Association will pay him $7.75 million across six years.
"This was a difficult decision, but one I feel was necessary for my family, the university, and, most importantly, the student-athletes," Marshall said in a statement. "I remain grateful for my years spent at Wichita State."
Marshall's resignation comes after the school launched an internal investigation into allegations that he physically and verbally abused former players and team staff during his 13-year tenure with the school.
The Shockers amassed a 331-121 (.732) record with Marshall at the helm since 2007. They also made seven trips to the NCAA Tournament, including a Final Four run in 2013.