The first successful effort to establish an Episcopal Church in Kansas was begun by the Rev. Hiram Stone. In late 1856, Rev. Stone resigned his rectorship in Connecticut after being appointed a domestic missionary to the remote field of the West.  On 10 December, two weeks after his arrival, a parish was organized in Leavenworth City. The church was named St. Paul’s in consideration of the support extended to the mission by St. Paul’s Church in New Haven, Connecticut.

It was a tumultuous time and place to begin a new parish. The organization of St. Paul’s took place only 2 years after the incorporation of Leavenworth, the first city in the territory of Kansas with a population of about 2,000.  Though the Army occupied Fort Leavenworth in 1827, this area of the country was previously set aside as Indian Territory by the U.S. government. However, the Kansas-Nebraska Act in 1854 opened the way for white settlement in this western expanse – with the stipulation that the settlers would vote on whether to allow slavery within the territory.  Resulting anti-slavery and pro-slavery agitation often led to open physical confrontation within the city and surrounding areas.

At the time of Rev. Stone’s arrival, there was only a small company of people favorable to our services, and among these only three communicants of the church.  For nearly two years, services were held in such places that could be procured in the town. On 5 September 1858, a wooden church, with a two hundred person seating capacity, opened for services.  Two months later, the Rev. Jackson Kemper, Missionary Bishop of the Territory, consecrated the church and three persons were confirmed. Another eight persons were confirmed by Bishop Kemper on 14 August 1859.  By the time of his resignation in October 1859, Rev. Stone listed forty-three communicants.

During the interval between his resignation and the arrival of the Rev. John Hobson Egar in March 1863, the little parish languished.  The congregation dwindled, the Sunday School was disbanded, and the frame church was lost. Upon assuming the rectorship, Rev. Egar took immediate steps to erect a building.  Though there were only 19 communicants in the parish at the time, three lots were purchased and plans for a church to seat about 500 people were obtained. Construction began in June 1863.  However, additional funding had be obtained from the east to complete the work. On 10 July 1864, the erected portion of the church was occupied for public worship for the first time. By 15 January 1866, the rector reported 53 communicants.

Shortly before Rev. Egar’s resignation in July 1868, the Parochial Report showed a good organ was in place, the building was lit by gas, lots were properly fenced, and the parish was almost out of debt.

Under the leadership of the Rev. John Kendrick, work to finish and enlarge the church was resumed in July 1871 and the building in approximately its present configuration was completed in 1872.

Following the Rev. Kendrick’s departure in 1874, St. Paul’s was served by another eight rectors through 1910, and another eight through mid-2018.  During that period, the church structure underwent a year-long restoration project in the late 1940s, and another major update in 2009, to include a new addition.