Ammons waived a 90-day notice of resignation Monday that would have kept him at the school until October, CNN reported.
The president's resignation came seven months after Robert Champion, 26, a drum major for the university band, died after being beaten on the band's bus during a hazing ritual.
Champion's family said last week that "the rampant culture of hazing found at FAMU would not and could not be eradicated without some major housecleaning of those who turned a blind eye to the problem."
The trustees passed a vote of no-confidence in Ammons' performance in June.
"I hear you loudly and clearly," Ammons told the board at the time. "I understand there are some measures that I have to take as president of this university to fix things, and I am going to fix them."