[1] As president of BYU, Brimhall helped institute the collegiate program, departments for specific subjects, and an emphasis on religious learning.

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.

[2]: 339  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.

[2]: 344 When Cluff left on an expedition to South America, Brimhall was appointed as the temporary superintendent of the LDS Church's schools and acting president of BYA.

[2]: 344  As acting president, Brimhall encountered many obstacles, especially with the funding of the school and the proposed Church University which threatened the existence of the Academy.

[2]: 499 Because BYA was being closely watched by the Board of Education and resources were scarce, Brimhall took it upon himself to ensure the success of the students.

[2]: 381–382  Following the pattern of LDS Church leadership, the board requested that BYU, Latter-day Saints University, and Brigham Young College appoint a presidency for their respective institutions.

[2]: 401  During Brimhall's time as BYU president, he helped organize the collegiate program into separate departments in order to increase concentration of certain subject.

In order to achieve the goals that he had set for BYU, Brimhall recruited educators who had degrees from prestigious universities in the East.

[5][2]: 418–427 [6] A similar controversy at the University of Utah in Salt Lake City — what Brimhall himself at the time described as 'a tempest in a teapot' — erupted four years later in February 1915.

There, the dismissals of two professors and two instructors by Joseph T. Kingsbury — and the subsequent resignations of 14 faculty members in protest (including Peterson, who earlier had resigned from BYU) — launched the American Association of University Professors' (AAUP) first institutional academic freedom inquest, spearheaded by AAUP founders Arthur O. Lovejoy and John Dewey.

[2]: 438, 443  Near the end of Brimhall's time as president, BYU began to emphasize its role as a religious institution, specifically focusing on the importance of testimony and morality.

[2]: 440  When the United States declared war with Germany in 1917, Brimhall conducted many patriotic assemblies and supported his students who enlisted.

[2]: 452 At a BYU board meeting, Brimhall announced that the church had asked him to devote some of his time to the seminary program.

In order to keep BYU running without Brimhall's constant supervision, a faculty executive committee would help with important school affairs.

[2]: 472 Suffering from chest and abdominal pain, Brimhall resigned the presidency of BYU in July 1921, although he remained head of the Department of Theology and Religion.