The history of Trinity Church is bound up with the development of the city of Atchison and the state of Kansas.  First organized in 1857 with the assistance of the Philadelphia Society for Missions in the West, the parish was originally named the Church of St. Mary Magdalene.  Before a building was constructed, the parish meet in homes, rented halls, and occasionally, the county courthouse.

Disagreements amongst residents in the territory of Kansas about the question of slavery were felt at the parish, and a number of members left to form a new parish called Grace Church.  This new parish, however, did not survive, and once a number of the members of Grace Church returned to St. Mary Magdalene, the parish was organized as Trinity Church.

In 1864, Trinity Church hosted the Fifth Annual Convention of the Episcopal Diocese of Kansas.  It was at this convention where Thomas Hubbard Vail was elected as the first Bishop of Kansas.  Vail also accepted an invitation to serve as Rector of Trinity Church, and so for several years, he served as both rector of the parish and Bishop of the Diocese.

Construction of a new building for the parish was completed in 1868.  The design of the building was based on the architecture of Calvary Church in Stonington, CT, which had itself been designed by the renowned church architect Richard Upjohn.

Over the years, a number of distinguished clergy have served at Trinity Church.  Four rectors have been nominated for election as bishops, and three of those four were elected to the episcopate.  One rector, the Rev. John Henry Hopkins, penned a hymn which was included in the most recent edition of the hymnal for the Episcopal Church.  Several rectors have served in various capacities at different cathedrals around the country.

Today, Trinity Church seeks to build on the legacy of its history by exploring the ways God is calling the parish to the faithful proclamation of the Gospel in this time.  We strive to be a parish where the glory of God is affirmed in our worship, the wisdom of God is evident in our discipleship, and the love of God is manifest in our outreach to the community.