Mark Zeigler of the San Diego Union-Tribune initially reported the news Monday.
Brian Dutcher will take over as the team's new head coach after being the "head coach in waiting since 2011." He has been an assistant under Fisher since his time in Michigan.
Fisher, 72, led Michigan to a national championship in 1989 and was the architect behind the Fab Five teams that went to back-to-back Final Fours in 1992-93.
He eventually joined San Diego State in 1999, taking over a team that went just 4-22 the previous season and had never won an NCAA tournament game. Over the next two decades, he turned the Aztecs into a consistent contender, totaling a 386-209 overall record.
San Diego State won six regular-season conference titles, four conference tournaments and reached the Sweet 16 twice under Fisher.
Although he had one more year remaining on his latest contract, he has decided to end his career after a 19-14 season.
Dutcher, 57, will now take over after working with Fisher in every season of his head coaching career.
For more news, rumors and related stories about Steve Fisher, San Diego State and college basketball, check out the college basketball and San Diego State streams on Bleacher Report's app.