In 1790 Samuel Weyburn, his wife and four children settled at a point of land on the west shore of Cayuga Lake. Four years later Richard and Benjamin Goodwin settled at the same place, now part of Taughannock State Park. Both families were Methodists and by 1795 the Revs. Valentine Cook, Thornton and Fleming were preaching in this territory. It was a usual custom, when two or more Methodist families settled near one another, to form a class. Often these classes were permanent and a church organization was started. In 1801, David James of the Seneca Circuit was preaching at Jacksonville and Goodwin's Point. Richard Goodwin was leader of the class. In 1804 another class was started with Benjamin Lanning as leader. In 1815 a class was formed at Mack Settlement (intersection of Perry City and DuBoise roads) with Elias Lanning as leader and in 1825 a church was built at Steven's Corners (intersection of Perry City and Krums Corners roads). That church was 25' x 34' feet and at one time the membership numbered one hundred. The building was later sold and moved from that location. 

The lot where the present Jacksonville Church stands was bought in 1826 for one hundred dollars. That deed for an acre of land also includes the land on which the school house stands. There were five trustees elected when the church incorporated, April 1, 1826. Joseph K. Owens, Silas Colegrove, Moses Gleason, Ebenezer Fairchild and Daniel Hankins. The "Old Colonial Church" was built in 1827. The bell was purchased in 1856 and the organ in 1873, both of which are still being used. December 18, 1878 the trustees voted to use the name "the First Methodist Episcopal Church of Jacksonville." Camp meetings played an important part in the growth of Methodism. The largest and most remarkable of these began in 1881 and continued each summer for several years. They were held in the A. B. Woodworth woods, now owned by H. Robert Bauchle on the DuBoise road. 

In January 1898 the "Old Colonial Church" was skid on oak planks pulled by teams of horses to its present site on the Jacksonville road. The cornerstone of the new church was laid May 24 and on November 23, 1898, the building was dedicated with four hundred people attending. Acetylene gas furnished lighting before the church and parsonage were wired for electricity in 1926. A new basement was added in 1930; the sanctuary was renovated in 1946. The golden anniversary and dedication of twelve stained glass windows was held May 23, 1948. The Rose Window in the west gable is in memory of James Monroe Mattison. The late Jessie (Mrs. Arthur) Agard compiled a church history for the 160th anniversary in 1955 and Florence Graham continued to update the history. The Jacksonville and Trumansburg parishes were combined in the 1940's under Rev. Arthur Moody. In 1967 they were again combined under Rev. Royal E. Filkins.