On the feast of San Luis Obispo de Tolosa, August 19, 1876, San Luis Obispo was incorporated as a city, and a small band of the Sisters of the Immaculate Heart of Mary established the first Catholic school on San Luis Obispo's Mission grounds. Located on MCP’s current site, the Academy of the Immaculate Heart offered both elementary and secondary education. In 1924, under the guidance of Reverend Daniel Keenan who was the newly appointed pastor of Mission San Luis and Diocesan Superintendent of Education, plans were made to erect a new parochial secondary and grammar school. The building was funded from a grant by the Hearst family. The grammar school, which occupied the ground floor classrooms, was commonly called mission School, in honor of the Spanish Padres. The new high school on the second floor was called Mission High School. The new collective Mission School was dedicated on August 19, 1926, the fiftieth anniversary of the founding of the Academy of the Immaculate Heart.
In 1957, Father William Scully, assistant pastor to Reverend Msgr. Patrick Daly, initiated the task of providing separate facilities for the grammar school and the high school. During the 1960’s the school operated under the name of Mission Central Catholic High School.
In June 1970, Mission Central Catholic was closed and Mission-Nativity grammar school was expanded to include ninth grade. At that time, the grammar school assumed operation of the high school building as the Junior High campus.
The dream of reopening the high school was born in the mid seventies. With the work of two Catholic laymen, Len Varni and Lyle Porter, a group of dedicated parents including Greg Morris, John Maulhardt, Larry Sage, and with the intervention of Reverend Jim Nisbet, Pastor of Mission San Luis Obispo, Bishop Thaddeus Shubsda gave full approval and re-dedicated the school, Mission College Preparatory, in August of 1983. The doors were opened in September of 1983 with eighty-six students. The first class to graduate from Mission College Preparatory Catholic High School was the Senior Class of 1986, sixty years after Mission High School first opened.
In 1999, a building project commenced to more than double the size of the school and to provide state-of-the-art science classrooms, computer facilities, cafeteria, gymnasium and locker rooms, professional space, and underground parking. The “new building” was completed in time for the 2004-2005 school year.
In 2008, construction began to provide seismic upgrades and renovations to the historic building that has served the school since 1926. Today, with its 350 students, MCP is administered under lay governance by Michael Susank, Principal.