St. Cyprian was designated a parish in June 1961 having been formed from sections of three older parishes: St. Martin in Sunnyvale, St. Simon in Los Altos and St. Joseph in Mountain View. Groundbreaking ceremonies were held on January 28, 1962 and until the church building was completed, Mass was celebrated in the rectory garage located then at 267 Gabilan Street in Sunnyvale. On March 17, 1963, Archbishop Joseph T. McGucken dedicated St. Cyprian Church. At that time, Father Thomas C. Reilly was named pastor.

In July 1965, Father John T. Gallagher was appointed pastor and it was at his direction that the first St. Cyprian Parish Council met on February 10, 1965. In August 1968, St. Cyprian School opened with three grades, a new grade being added each subsequent year.

The Shrine of Our Lady of Guadalupe, located near the present rectory was a gift of the Davila family and was dedicated in September 1967.

Succeeding pastors have been: Father Patrick Kean (1977-1981); Father Jim Walsh (1981-1989); Father Lawrence Hendel (1989-1996); Father Mark Neary (1996-2000); Father Tim Kidney (2002-2004); Father Arthur Yabes (2004-present).