On January 14, 1893, a deed for 1.5 acres was granted by Mr. J. G. Cone to the Methodist Episcopal Church, South. The present church was built on this site in 1895, with lumber donated by Mr. James W. Wright. The church was called MacDonnell until 1921 when the name was changed to Hubert for the community
. Prior to 1952, worship services were held once each month at three o'clock in the afternoon. Under Rev. J. D. Corbitt, Jr.'s pastorate, the worship service was changed to every Sunday morning. New windows were installed in 1956, and, in 1958, the church was completely remodeled. The social hall and education building was purchased from the Board of Education in 1959. While Rev. Harold Brooks was the pastor in 1961, Easter sunrise services began with breakfast prepared by the men of the church on the outdoor grill. A new hardwood floor, carpet, and pews were installed in 1965. Central heating and air conditioning were added in 1969. In 1970, bathrooms were added to the education building and, in 1974, pulpit furniture was donated by M. L. Miller, Jr., Dr. and Mrs. W. M. Cone, and Rev. Carlton Reid. The Centennial Anniversary of Hubert UMC was held on July 24, 1977, with the Rev. Vernard Robertson, whose ancestors helped found the original church, delivering the dedicatory address.
In 1924, Hubert was listed on the Guyton Charge along with Pineora. It remained on the Guyton Charge until 1962, when it was put on the Meldrim-Ellabell Charge. On October 1, 1974, this church was added to Brooklet as a satellite church. At the charge conference in 1980, the decision was made to name the charge, Brooklet-Hubert UMC Charge.