The school said Friday that the contract replaces the final two years of Hayford's previous deal.
In three seasons at the school, Hayford is 40-54 overall and 25-31 in the Big Sky Conference. The Eagles were 15-16 overall and 10-10 in the Big Sky last season.
Hayford is 294-138 in 15 seasons as a college head coach at Sioux Falls, Whitworth and Eastern Washington.
