Dooley, 47, takes over a program that was the darling of the 2013 NCAA Tournament when the Eagles became the first No. 15 seed to advance to the Sweet 16 round of the tournament. FGCU was 26-11 on the year.
That success caught the attention of several coach-seeking schools, including Southern California, which hired Coach Andy Enfield away from FGCU.
Dooley was the head coach at East Carolina from 1995-99, building a 57-52 record. He was most recently an assistant to Kansas Coach Bill Self for 10 seasons and previously was on coaching staffs at South Carolina, East Carolina, New Mexico and Wyoming.