The church had its beginnings in 1828 when a little group of men and women in Castleton (now Seneca Castle) met and eventually organized as Methodists. They were invited to join the Presbyterians but preferred to follow their own creeds. They met at the old log schoolhouse for prayer meetings every two weeks.
In the early days they were served by circuit rider preachers. Following the Presbyterian revivals in 1829-1832 six young people joined the Methodists and were baptized in Flint Creek. By 1840 their numbers grew to 49. They had outgrown the schoolhouse and the brethren decided to build a brick church. There was clay for bricks on a nearby farm. one member molded the brick, others did team work, carpenter work, and laying brick. One of the young members polished every brick for the front of the church by rubbing one brick on another. The Methodist church was dedicated in 1842. In 1870 the church was slightly enlarged. In 1914-1915 the main church building was enlarged. There, also, was an addition to the east side of the church, which was reconstructed, on the interior in 1976.
In the 1860’s the Orleans Methodist Church met at the Seneca Castle Methodist Church. In 1821 they shared the minister with the Flint Methodist Church for a short time and again for about a year in the 1960’s. An effort was made to unite with the Presbyterian church in town in 1953 and again in 1964. The efforts failed causing the Presbyterian church to close in 1965.
The Seneca Castle Methodist Church actively participated in the Seneca Rural Council of Churches for 25 years. The council consisted of area rural churches of various denominations.
Since the organization of the Sunday School in 1836, this program has been an important part of the church from nursery to adults. The declining birth rate has affected the church as it has schools. The Sunday School program still exists to meet the needs of the available age groups.