The date of organization is thought to be 1868, with the first building erected in 1872. The first pastor was Rev. John W. Talley. After the first building was destroyed by a storm in 1876, a new wooden structure was built. Members worshiped in the Presbyterian Church during construction.
In 1909 the building was brick-veneered but was partially destroyed by fire in November 1945. Under the leadership of Rev. Albert W. Ray, the present brick building was erected in five months. The building was large enough that eight Sunday school rooms and a fully-equipped kitchen were also added. The congregation worshiped in the Primitive Baptist Church during this time. During the late 1960s and early 1970s, new carpet and air-conditioning were installed, a new organ was purchased, and the Parsonage was remodeled and updated. Boston UMC celebrated its Centennial on May 7, 1972, and was voted Church of the Year in 1985.