In 1851, the University of the Pacific was established under the auspices of the Methodist Church in Santa Clara, California. As early as 1856, the University was divided into the "University of the Pacific" and the "Female Collegiate Institute", with music as a course offered only to women. By 1878, the University was integrated, and the newly designated School of Music registered 32 students in four categories:
- an elementary class for beginners
- an amateur class for "those who devote chief attention to other branches of instruction in the University"
- a preparatory class
- an artists' class
The catalog for 1882-1883 specified music admission requirements and the first bachelor of music degrees were awarded in the mid-1880s. The first theory of composition major graduated in 1909, and Pi Kappa Lambda and Mu Phi Epsilon were established in 1919.
The University moved from San Jose to Stockton, California in 1924 and the Conservatory became a charter member of the National Association of Schools of Music in 1928. As the respective divisions in music, art, and drama became larger, they were made independent departments in the University. Phi Mu Alpha was established in 1931 and Pacific Music Camp in 1946.
A highlight of the 1950's was a performance of the University Symphony Orchestra at the Brussels World Fair (1958). This appearance was by invitation from the U.S. State Department.
The Pacific Music Clinic (1951-1984), brought thousands of high school orchestra, band, and choir students to Stockton once a year for a combined performance.
In 1978, a series of special events marked the Centennial Celebration of the Conservatory of Music. Alumni Dave Brubeck returned to present two concerts and one of the Conservatory's former deans, Howard Hanson, conducted the University Symphony Orchestra and Chorus in the West Coast premiere of his "Sea Symphony".
A degree in Music Therapy was initiated in 1981 and in 1983, a Bachelor's Degree in Music Management was accredited by the National Association of Schools of Music.
The Brubeck Institute was established in 2000 for the study, promotion and performance of American music.
The 125th anniversary of the Conservatory was celebrated in 2003 with a sold-out performance of Beethoven's 9th Symphony performed by the University Symphony Orchestra & Chorus in the Faye Spanos Concert Hall.
The 135th anniversary of the Conservatory will be celebrated in 2013 with a repeat performance of Beethoven's 9th Symphony.