In 1857 when Kansas was still a territory, Reverend Charles Reynolds conducted the first Episcopal religious services held in Lawrence at the request of his brother Samuel, one of the early settlers of the town. The reverend decided to return to Lawrence in 1858 with his family in order to establish an Episcopalian church.

Trinity became the 8th Episcopal church organized in territorial Kansas and by summer 1859 had its own building on Vermont Street. The parish survived the hardships of the Civil War and continued to grow, to the point that the building needed an addition in order to serve all its congregation by the mid-1860s. By Easter 1873 the congregation had an entirely new church built, its membership now numbering well over 100 people.

In April 1955 the church building caught fire, its interior almost entirely destroyed, including the roof. Parishioners were able to rescue several objects, including the altar cross and other altar pieces. The renovated church reopened a year later in March 1956.

In the late 1980s Trinity's leadership started exploring the idea of building another parish church in the developing western end of the city. By spring 1996 St. Margaret's Episcopal Church had its groundbreaking ceremony.