St. Paul's was officially organized as a mission on June 8, 1958, by Bishop Edwin A. Penick, with 20 families led by its first deacon, Roderick L. Reinecke. Services were held in the band room of Cary High School (now Cary Elementary), as parishioners began acquiring church "furnishings" and building the altar and kneelers themselves.

During the tenure of the second deacon, C. Waite Maclin, land was purchased at the current location on Union Street.

In August 1960, parishioners began erecting their new church home, a steel building now known as the "tin building." A brick Education Building was dedicated in 1973. This building is being renovated into a nursary, expected to open around Easter of 2008.  The tin building was used for some years as a meeting site for the AA, scouts, and other groups, but finally had to be torn down in 2004 to make room for the current worship space.

Mr. Maclin was followed by another deacon, Samuel Moore, who like his predecessors became a priest while at St. Paul's. Each time, ordination to the priesthood was followed by a calling to serve a different church. St. Paul's first Priest-In-Charge who actually was a priest was The Rev. Mr. Donald W. Fraser (1966 - 1968). During his tenure two trailers were loaned to St. Paul's by the Diocese for use in the Christian Education program, and an addition was built onto the east end of the tin building to serve as a sacristy.

Rev. Frazier was followed at St. Paul's by The Rev. Frederick F. Valentine, Jr. (1969 - 1974). Rev. Valentine worked to ensure that new members to St. Paul's quickly became involved in church activities and leadership. The vestry was enlarged to nine members, and planning committees abounded. The appointment of the first woman Senior Warden, Gert Ferenczi, and the establishment of a new, more successful choir were some of the noteworthy events in this period.

In 1975, the Rev. William Coolidge began his leadership of St. Paul's Mission. By 1976, St. Paul's was granted parish status by the Diocese. With Rev. Coolidge's focus on pastoral care and counseling, the small church grew, prompting the need for a new church building. Although Mr. Coolidge departed in February 1981, the parishioners moved forward with the building plans in the interim period and a new church was completed. During this same period, a search for a new rector was conducted.

On October 31, 1981, St. Paul's Parish welcomed the Rev. Charles Hocking and consecrated the church. Fr. Hocking brought a more formal manner to St. Paul's. He promoted the Anglican philosophy of "Via Media," the middle way, in which people of all viewpoints are welcome to worship together in one church. St. Paul's still reflects this philosophy today.