In 1837, the Rt. Rev. Jackson Kemper, the first missionary bishop of the Episcopal Church arrived at Fort Leavenworth in "Indian Territory". He was the first ordained minister of the Episcopal Church to set foot on Kansas soil.
In 1856, the Rev. Hiram Stone heard one of Bishop Kemper's fervid appeals for help in his vast field and volunteered his services. On December 10, 1856, he announced the organization of Saint Paul's Church, Leavenworth City, the first permanent Episcopal organization in the Diocese. A neat wooden church with a capacity of seating two hundred person opened for service on September 5, 1858. Bishop Kemper visited the parish on August 14, 1859 and confirmed eight persons.
Fr. Stone resigned in October 1859. During the interval between his resignation and the arrival of Reverend John Hobson Egar in March 1863, ,the parish languished. The congregation dwindled, the Sunday School was disbanded, and even the small frame church was lost. Upon assuming the rectorship, Fr. Egar took steps immediately to erect a building. Three lots were purchased, plans for a church to seat about 500 people were obtained and construction commenced in June of 1863.
On Sunday July 10, 1864, the first public worship in the new building was held. Work to finish and enlarge the church was resumed in July 1871 and the building in approximately its present configuration was completed in 1972.