Head coach Steve Renfroe made the announcement on Tuesday prior to Auburn's regular season home finale vs. Mercer.
"We appreciate everything Mark has done for this program over the last four seasons," Renfroe said. "Mark is a true Auburn man and we wish him the best of luck in his future endeavors."
Fuller, a former pitcher for the Tigers, came to Auburn after spending three seasons as an assistant coach at North Carolina State. He is a 1992 Auburn graduate.
"I have decided that it is time for me to pursue other opportunities that will allow me to spend more time with my wife and two sons," Fuller said. "I want to thank Coach Renfroe for the opportunity during the past four years to coach at my alma mater. It has been a great experience."