In 1810 local Anglicans founded Trinity Episcopal Church to fill the need for worship in the town of Upper Marlborough. Churches as close as St. Thomas and St. Barnabas were a long carriage drive away over rough and often impassible roads.

On August 13, 1810, the newly formed vestry elected the Rt. Rev. Thomas John Claggett as the first rector of Trinity Church. Bishop Claggett was the first Episcopal Bishop to be consecrated in America. Bishop Claggett established his new Marlborough church in an abandoned wooden Presbyterian building built in 1704. In his Notitiae 24 May, 1809 to Jun 1810, Bishop Claggett sounds pleased: "Public worship is well attended here, the responses are audibly made by almost the whole of the congregation, and the rubrics are still more pleasing, an evident reformation in the manners of this people hath certainly taken place."

It was not until July 16, 1812, that Bishop Claggett officially consecrated Trinity Church. It was a time of great upheaval. Margin reference notes in the vestry minutes of May, 1814, indicate that British troops camped in the church, tore out pages from the minutes book and prevented the vestry from meeting. Bishop Claggett served as rector until his death August 3, 1816.

By 1846, the congregation had outgrown the original frame building and the vestry contracted to build a new church at a cost of $4,000. On December 31, 1846, the Rt. Rev. William R. Whittingham, Bishop of Maryland, consecrated the present brick building. The Prince George's Enquirer writes, "The pews were distributed by lot; all who subscribed $100 or more having had the first choice, and next those who paid $50. Ten free pews were designated by the Vestry."

In 1896, the bell tower was added to the front of the church. In 1975 a bequest from Charles Clagett made possible the construction of the Clagett Building which is connected to the church by a covered walk. In 1985 under the Rev. Halsey Stevens III, restoration of the church building began, and on January 4, 1987, the completely restored church was rededicated by the Rt. Rev. John T. Walker, Bishop of Washington.

The grounds surrounding the church have been used as a cemetery since the old Presbyterian congregation worshiped at the site. The oldest grave bears the name of John Moore, a soldier in the Revolutionary War who died in 1793. The present Trinity Cemetery on Rectory Lane was established in 1885 and enlarged in 1939.