In early January 1947, Denver Archbishop Urban J. Vehr granted Father Edward Dinan permission to say Mass and “administer whatever sacraments might be necessary or useful” in Flagler. Father Dinan was traveling to Flagler once a month from St. Charles Church in Stratton. By the end of that same January, Father Dinan had a plan in place to purchase a school building for $1,775 and have it moved to Flagler. The people in Flagler signed up to furnish the foundation for the building. Archbishop Vehr pledged $500 for “either the construction work or for the furnishings of the interior of the chapel.”

After the construction of the foundation and addition of a vestibule, the church was ready for the first official Mass on Oct. 26, 1947. Father Dinan reported that approximately 75 people attended Mass every Sunday. By 1952, Father Dinan was in the early stages of planning for a school. In July 1959, St. Mary Parish got a new church, as was reported by The Flagler News.

Father George V. Fagan, JCL, served as pastor of St. Mary from 2002-2020. Father Tomasz Jamka was appointed pastor in July 2020. Father Jim Klein was installed as pastor in August 2023. Father Paul Williams was named parochial administrator in July 2024. Benedictine Father Sijo George was named pastor effective July 1, 2025.