Prior to 1983, The Prince of Wales area was part of the greater Diocese of Juneau Missions. In 1925, Bishop Joseph Crimmont designated northern POW as a mission assigned to St. Rose in Wrangell, and southern POW under the designation of St. John the Evangelist to Holy Name in Ketchikan. Activity and visits were intermittent until the Diocese, under the guidance of Bishop Michael Kenny, assigned full-time ministers to the Island. Records are hazy as to when Sister Nadine Grogan was assigned, but she and Father Michael Nash began the "real" history of the Catholic community now known as St. John's by the Sea.

Father Nash was assigned September 1, 1983, as the first priest serving Prince of Wales Island and the surrounding island communities. A licensed pilot, he used his airplane in his ministry and from his base in Thorne Bay, made true outreach a reality. Sister Nadine was stationed in Craig and together they made the Catholic Church a presence in the local communities. They laid the groundwork for the parish that evolved from their ministry.

Sister Laetitia Lariviere arrived in August of 1987, and Father James Blaney arrived within the same year. At that time, the Catholic faith community was using the Presbyterian Church facilities in Craig for worship services. Property had been acquired in Klawock, however, and the church building project gained momentum. Many hands and many talents working together conceptualized, designed, and created a center for the Catholic community, a place for worship and education, for hospitality and sharing. Bishop Kenny blessed and dedicated the new church on April 28, 1992; thus, the mission had become a parish.

With a physical center, the Catholic community became a more visible presence on the island, drawing in new members. In 1999, after more than ten years of relative stability and growth, the community experienced several changes in staff in rapid succession. Father Jim was reassigned to work with the Northern Missions and was replaced by Father Edward Matthews. Sister Tish moved on to new challenges with her home community. As one of the founders of POWER (Prince of Wales Emergency Resources), an organization giving food, heating assistance and material goods to those in need, her legacy reaches far beyond the Catholic community.

April 2000 brought a new ministry team: Sister Zita Simon and Father Jean Paulin Engbanda-Lockulu. During their ministries the parish hall was added, including classrooms and another apartment to house both ministers on-site.

Fr. Jean-Paulin remained at St. John's until his transfer to St. Gregory's Parish in Sitka, in June 2003.  Sr. Zita remained at St. John's as the only full-time minister, while Fr. Ed Penisten, then from Holy Name Parish in Ketchikan, traveled to the island to celebrate mass when possible.

In August 2004, Sr. Zita departed Prince of Wales Island to take a new position within the Diocese. Fr. Perry Kenaston became the new, sole full-time minister at St. John's by the Sea, after five years of service to the remote communities in the Diocese's Northern Mission.

Since its humble beginnings in 1983, St. John's by the Sea has faced many challenges not unfamiliar to remote parishes. Our ministers have persisted in leading parishioners to worship, despite the logistical challenges of travel and weather on Prince of Wale Island. "Church" takes place in large and small groups, in remote areas and in cities, in churches, school gymnasiums and living rooms. Whether a full mass celebrated with a priest, or a communion service offered by a commissioned parishioner in the absence of a priest, St. John's by the Sea parish has grown through the love of God and the grace of community. Blessed with those gifts, it will continue to spread the Good News.