Saint Philip Neri Parish began with the authorization of Archbishop Edward J. Hanna in 1925 with the first and founding pastor Fr. Maurice O'Keefe. The parish is situated in the east end of Alameda atop part of the ruins of an ancient village once occupied by a branch of the Miwok Indian Tribe. In 1959, the original church was converted into the parish hall (O'Brien Hall), and a new church, convent (now the annex), and school was built under the leadership of Fr. O'Brien. 


Saint Philip Neri Catholic School opened its doors in September 1959 and was staffed with the Sisters of Notre Dame de Namur, with Sr. Matilda Carmel as its first principal. It began with grades 1-4, and added one grade each year until it saw grades 1-8 in operation by 1963.


In 1974, the Notre Dame Sisters were recalled due to personnel shortages, and the Dominican Sisters of Adrian, Michigan, took over. In 1977 Sr. Laura Mary became principal and served until 1983, when Sr. Laura Marie replaced her. Monsignor O'Brien retired in 1985 and was replaced by Fr. Breton as pastor. In 1991, Fr. Jerrold Kennedy arrived and was pastor until 1998. It was also in 1991 that the Adrian Sisters left the school, and lay principals have served ever since.


Today, the school hosts a media center for broadcasting and media classes, a state of the art science lab, a beautiful library, and an outdoor garden.