He replaces Cameron Dollar, who was fired earlier this month after eight seasons at Seattle, during which he led the Redhawks through their transition to full Division I status. Dollar was unable to turn Seattle into a contender in the Western Athletic Conference.
Hayford was 106-91 in his six seasons with the Eagles, including a pair of 20-win seasons. Hayford took Eastern Washington to the NCAA Tournament in 2015 for the second time in school history.
"I humbly move into this position with a desire to lead a championship program that graduates outstanding leaders," Hayford said in a statement. "The history of the basketball program here is rich and unique. We will work tirelessly to build a program that will return Seattle University to the NCAA tournament."
Prior to going to Eastern Washington in 2011, Hayford spent 10 seasons as the head coach at Division III Whitworth in Spokane, Washington, turning the Pirates into a powerhouse at the lower level.
"Coach Hayford has a history of success in developing programs that compete on the national level," Seattle athletic director Shaney Fink said. "He is a proven winner, a committed educator and a passionate leader, and we are excited for him to bring that blueprint of success here to Seattle U."
Eastern Washington moved quickly to replace Hayford, promoting assistant Shantay Legans to the head coach position full time. Legans has been an assistant at Eastern Washington for the past eight seasons.
Earlier this week, Washington hired Dollar for a second stint as an assistant coach with the Huskies. Dollar, who was 107-138 in his time at Seattle, spent seven seasons as an assistant for the Huskies from 2002-09.