Flanagan is being investigated by ISU police after a former campus employee accused him of assault.
He stepped down during a special Board of Trustees meeting Saturday. The resignation took effect immediately.
A statement on the university’s website says Vice President for Student Affairs Larry Dietz was named to replace him.
It includes a brief statement from Flanagan in which he says he appreciated working with students and faculty but that after discussion with the board he’s decided it would be best to “pursue other opportunities.”
The complaint filed against him, accuses Flanagan of assaulting a former employee while complaining about the care of the president’s lawn.
ISU Chief of Staff Jay Groves said the university would have no additional comment.