Built in 1962 under the direction of Father David Melbourne and then Bishop Dermot O'Flanagan, St. Paul the Apostle Catholic Church, located in the Mendenhall Valley, began as a mission of the Cathedral of the Nativity of the Blessed Virgin Mary, 10 miles distant in downtown Juneau, Alaska. As a mission, St. Paul's was served by priests from the Cathedral. With the building of St.Paul's Church came the official recognition of the strong and growing Catholic community that lived in the Auke Bay and valley areas of Juneau.

Since the mid 1940's, the out-of-the-road crowd had been holding home masses served by priests from the Cathedral. Many of the Catholic children attended St. Ann's Elementary School in downtown Juneau, where they received their religious education. As the community grew, so did the search for a larger facility for celebrating mass. The Coast Guard building at Auke Bay was tried and then rejected as a suitable gathering place. It seems the building was poorly heated that the water froze in the cruets.

In the early 1950's, the community purchased land from the David and Maybelle Horton family at Auke Bay to build a church. The site was prepared and footings poured, but the church was never built because of the rapid population growth in the airport area. The Horton family bought back the land in 1955 and later built Horton's Hardware on the site. St. Paul the Apostle Church was finally built on the Atlin Avenue property donated by the Roger and Mary Hurlock family. Approximately 100 families attended St. Paul's Mission, which seated 200 people.

The steady population growth of the Mendenhall Valley, Auke Bay area and beyond prompted Bishop O'Flanagan, in June of 1968, to declare St. Paul's an independent mission of the Cathedral. Father Matthew E. Hoch was named priest-in-charge of St. Paul's and took up residence there in the rectory attached to the church. Lemon Creek became the boundary to divide the mainland between the Cathedral Parish and St. Paul's Mission. Bishop O Flanagan further delineated the boundaries of the mission as Lemon Creek on the south, a direct line between Mt. Fairweather and Mt. Nesselrode on the north, Lynn Canal on the west, and the coastal mountains on the east. Though these parish boundaries may still exist, people today attend the parish of their choice, many without the knowledge that such boundaries are on the books.

By June 1969, Father Hoch had added a cross and a cemented front access to the church. He also established a parish council. Father John Lunney filled in during 1970 at St. Paul's Mission. Father Thomas Sloan also served at St. Paul's for about ten months in 1970 and 1971, during which time a trailer was used for the rectory. About this time, the people of St. Paul's began asking for their mission to be made a parish.

On January 25, 1972, the feast of the Conversion of St. Paul, St Paul the Apostle Mission was separated from the Cathedral Parish and established as a parish by then Bishop Francis T. Hurley.

Father Leo McCaffery, who had been at St. Paul's since July of 1971, was named the first administrator of St. Paul's Parish. His tenure was short. Father Peter Gorges received his assignment as the first pastor of St. Paul's Parish in October, 1972. He remained as St. Paul's pastor until 1981.

When St. Paul's became a parish, approximately 150 families belonged to the parish community. A need for classrooms and a parish hall for religious education, meetings and social events became quite evident. Religious education classes were held in private homes and in rented classrooms. Under Father Gorges' direction, a parish hall with large room to seat 200 people and a kitchen upstairs and an office downstairs was constructed. A rectory was also built to replace the trailer of many years use. Completion of the project occurred in 1978.

In 1981, Father Gorges handed the reins of St. Paul's to Monsignor Charles Kekumano, who shepherd St. Paul's until 1984. Father Michael Nash was the associate pastor during that time. In 1984, Father Bill Finn stepped in, along with associate Father Ben Konda, to guide St. Paul’s faithful.

By 1985, St. Paul's Parish had grown to 504 families and had begun to feel the pinch of space. Religious education classes for children had spilled over into the rectory and the senior center, built on church property. Four Eucharistic celebrations were needed each Sunday to accommodate the larger parish family. St. Paul's had become the largest parish in all of Southeast Alaska.

Monsignor James Miller came to St. Paul's as pastor in 1986 and remained until 1994. Father Vic Capriolo served as associate pastor from 1988 to 1991. In the years from 1987 to 1989, St. Paul's added a wheelchair ramp to the front of the hall and a new, sloped cement slab to the front of the church. A handicap-accessible bathroom and an elevator were also installed for the parishioners' convenience. Also, a parish office and a sacristy were added to the back of the church to free space up for other parish needs. Beginning with the 1992-1993 school year, children's religious education classes ran three sessions each week to make room for all the enrolled. Also, the sanctuary was enlarged to allow space for the choir and extra seating for parishioners.

In 1994, Father Michael Hayden became pastor of St. Paul's. Father Pat Travers assisted as the associate pastor. That year, St. Paul's added a Spanish Mass to their weekly Eucharistic celebrations, expanding weekend masses to five. Sister Carol Crater also began helping at St. Paul's during this time. Father Hayden split the parish council into a pastoral council and a finance council for smoother running of parish affairs. In 1995, Father Pat Travers was named administrator of St. Paul's, with Father Jef Johnson, OMI, as priest-in-residence. In late 1995, Father Jef Johnson was named administrator of St. Paul's and, finally, in spring of 1996, pastor. In 1998, Father Tony Dummer, OMI became the pastor of St. Paul's and remained until 2007. In 2007, Father Scott Settimo served as the pastoral administrator for three months. On that same year, Father Tony Dummer handed the reins of St. Paul's to Father Pat Travers. In 2015, Father Jean Paulin Lockulu began to shepherd St. Paul's.

Permanent Deacons George Michaud, Jerry Jones, Pat Benigno, Paul Paradis, Gary Horton, Mike Monagle, Steve Olmstead and Jeff Volkers have served in various roles at St. Paul's Parish from 1974 to the present.

St. Paul's rapid growth of the late seventies and early eighties slowed but steadily crept higher. It is a culturally diverse parish, with fairly transient population. In 2001, St Paul's built a new church. St Paul the Apostle Catholic Parish looks forward to many more faith-filled years to come.