Mary Jane Saunders sent a letter Tuesday saying she would step down and return to the FAU faculty, The Miami Herald reported.
Saunders' tenure was marked by a series of controversies, including renaming the football stadium for the private prison company GEO Group, which had donated $6 million. The proposal sparked the nickname "Owlcatraz" in a bow to the school's mascot.
The Herald said communications Professor James Tracy sparked outrage by espousing conspiracy theories suggesting both the Sandy Hook Elementary School massacre and the Boston Marathon bombings were staged events. A third controversy involved a professor accused of leading a "Jesus stomp" classroom exercise.
"There is no doubt the recent controversies have been significant and distracting to all members of the University community. The issues and the fiercely negative media coverage have forced me to reassess my position as the President of FAU. I must make choices that are the best for the University, me and my family," Saunders wrote.
The university Board of Trustees accepted Saunders resignation and said she would be assigned a special research project to determine the feasibility of starting a physician's assistant program.