The school was first opened in 1893 for 20 students.
In 1911, the Fallbrook High School board voted for a $20,000 20-year bond for construction of a new high school.
In the 1930s, the Public Works Administration Project approved a grant of $34,000, 45% of the cost of a new auditorium-gymnasium-cafeteria, a pool and grading of a sports field.
In 1934–1938, the student body voted on the school colors of red and white. The athletic teams were named "The Warriors" in honor of the large number of Native-Americans in the student body.
In 1939, Fallbrook Union High School was rated the most outstanding high school in the country by Chicago Farm Foundation.
In 1946, the State Department of Education rated Fallbrook to be the best small high school in California.
In 1948, the State of California declared that the main part of the school building did not meet earthquake standards and was condemned. A new building was built the following year.
In 1953, a $325,000 bond was passed to move the school to a site south of town. The 46,000-square-foot project was delayed due to county-wide strikes by brick masons and an unusually rainy year.
In 1967, a $900,000 bond was passed to add a cafeteria, classrooms and bus-loading facilities.
In 1994, a $23 million bond to improve the facilities and to ease the overcrowding problem was approved by Fallbrook voters. The project included a new gym, performing arts center, agriculture center, media center and vocational arts buildings.
Dr. Robert Thomas also retired in 1994 and Joe Diminicantanio was appointed superintendent. Enrollment had reached an all-time record of 2,300 students.
Construction began during summer 1996 on the five new buildings. Included are a $3.3 million, 27,000-square-foot gymnasium; $5 million performing arts center; $834,000 agricultural center; $4.5 million media center and a $2 million vocational arts building. The project took almost 6 years to complete with the last building opening in the fall of 2000. The impressive Bob Burton Center for the Performing Arts is a joint community-school facility and is named after Bob Burton, the Student Activities Director of thirty years.
In 1997, Diminicantanio retired and Thomas Anthony was appointed as superintendent.
As of 2007, the Fallbrook High School campus is home to a wide range of comprehensive high school offerings and is also home to Oasis and Ivy High School. Collectively the campus provides educational facilities for more than 3,000 students.
In 2016, district residents approved issuing $45 million in bonds for upgrading classrooms and facilities and improving school security. The initiative was passed by 64.75% of voters.