In October 1887, the principal of the Royal Academy of Music, Sir George Macfarren, died, and in early 1888 Mackenzie was appointed to succeed him. He held the post for 36 years until his retirement in 1924. At the time, the Academy was overshadowed by its younger rival, the Royal College of Music, and Mackenzie set about reviving its reputation. He was fortunate in enjoying the friendly support of his opposite numbers at the College, George Grove, and, from 1895, Hubert Parry, and the two institutions established a close working relationship of mutual benefit. In addition to overhauling the curriculum and reorganising the faculty, Mackenzie engaged personally with his students by teaching composition and conducting the student orchestra. In 1912 the Academy moved from its old buildings in Mayfair to purpose-built premises in Marylebone. In his later years as principal, Mackenzie became markedly conservative, forbidding his students to play the chamber music of Ravel, which he stigmatised as "a pernicious influence".