Hillsboro Methodist Episcopal Church” was organized in 1807. It belonged to the Haw River Circuit at its beginning. The first preaching services were held in the old courthouse, since no church building had been erected at that time. In 1821, a letter written by Rev. Henry Hardy states “a camp meeting was held in Hillsboro, and about thirty-eight joined the Methodist faith. They opened a subscription for the purpose of raising funds to build a house of worship.” Land was bought from James Webb upon the condition that “a Meeting House upon the said lot for the use and benefit of the Methodist Episcopal church.” The church used a wooden house on this property as the first church building.

When the wooden church began to show signs of wear, the members bought the present land from Henry N. Brown in 1859 for $200. Money was raised to build a new church and Captain John Berry was given the contract. He took the old church building as part payment for the job. HUMC is the only church in Hillsborough known certainly to have been designed by Captain Berry.

The new building was completed in 1857. Its high elevation, tall windows, tower, and steeple make it a graceful church building. Captain Berry's use of white trim against red brick gives it a Georgian quality and definitely relates it to the old courthouse. The louvered shutters, galley, original pews, and antique pulpit with fluted columns give interest to the interior of the church. The original building (sanctuary/narthex/balcony/basement) designed by Captain Berry remains intact. When the church was built, the floor slanted down toward the pulpit. A large stove was located at the back of the church. There was another stove where the organ is now located. The pews and pulpit date back to this time.

A local legend tells that during the Civil War, when the Confederates found that they needed more cannons to hold their lines, they asked the church to donate the bell to be melted and added to their cannon supply. The church declined the proposition.

The new Methodist Church was dedicated by Rev. William Barringer, Presiding Elder of the Raleigh District, on October 6, 1861. The text was taken from Colossians 1:27, "Which is Christ in you, the hope of glory; Him we preach." The first sermon preached in the present church sanctuary was by Rev. Jesse A. Curringgins from Psalms 51:12, "Restore unto me the joy of thy salvation."

An educational building was added to the original building in the 1940s. There once was a swimming pool in the back yard of the church that was used by community children. Duke Divinity students often found themselves supervising this pool when serving the church during the summer Duke Endowment programs. The pool was filled during the 1960s.
A separate structure located at the far end of the church property was called the “Scout Hut” and was built primarily for the Boy Scouts' use. It served this purpose for many years until the Scouts were given a house on Wake Street. In the 1970s, this building was completely renovated for church use. A kitchen and upgraded bathroom was added, thus making it into a multipurpose unit, named the “Ruth Room” by the church leaders. A small room in this building was converted into the Mark Prayer Chapel.