In 1890, Abraham O. Smoot invited Brimhall to be a part of the faculty at BYA as a church calling. Through BYA and with special instruction from Benjamin Cluff, Brimhall was finally able to complete a college degree, while simultaneously heading the Intermediate Department and Preparatory School. When Cluff became BYA's principal , Brimhall took his place as head of the Normal Department, but continued in his position over the Training School as well. Then in 1894, Cluff returned to Michigan to complete his graduate work and left Joseph B. Keeler and Brimhall as co-acting principals of BYA. Both Brimhall and Keller had desires to follow Cluff's example and go east to study, but because Keller had been at BYA longer, he was permitted to go east first. Because of this delay in Brimhall's education, he would never again have such an interest in pursuing higher education. This became one of the greatest weaknesses of his administration.