The Parish was established on February 23, 1946 by The Most Reverend Charles F. Buddy, Bishop of San Diego, to serve the Catholic communities of Encinitas, Cardiff, Leucadia, and Olivenhain. The First Pastor was Rev. Patrick H. Linneman whose mission was to build a fitting house of worship.

As the Parish community grew the need for a Parochial School became evident.  Under the direction of Father John Bradley, St. John’s School opened September 10, 1957 with an enrollment of 182 pupils under the supervision of the Benedictine Sisters of Tulsa Oklahoma.