The school announced Dooley's hiring Wednesday, saying he agreed to a five-year contract.
It is Dooley's second stint as the Pirates' head coach. He went 57-52 in four seasons with East Carolina from 1995 to 1999, before he was replaced by Bill Herrion.
Dooley took over for Andy Enfield as the Eagles' coach in 2013 and went 114-58 with three Atlantic Sun regular-season championships and NCAA tournament berths in 2016 and 2017 for Florida Gulf Coast.
Jeff Lebo stepped down six games into his eighth season at East Carolina. Interim coach Michael Perry finished the year, and the Pirates went 10-20 for their fourth straight losing season.