The original schoolhouse was located on the northeast side of Main Street, on the present site of the Lee Center Methodist Church. In the 1860's a new road (Church Street) was put in next to the school to connect Main Street to Sulphur Springs Road to make travel to the Eames Tannery easier.

On May 1, 1871, one acre of land was purchased from Jay Capron for $300 in anticipation of building a new school house. This land was located a block south of the original schoolhouse, at the end of School Street.

On August 9, 1871, a contract was let to Cornelius Dingman to build a new schoolhouse. Work began on September 8, 1871, and the Union Free School, District No. 3, opened on January 9, 1872. William P. Robinson was the first principal. The old schoolhouse on Main Street was dismantled and rebuilt on a new foundation next door to the Lee Center Methodist Church and was used as a parsonage. This building, along with the Methodist Church, was totally destroyed by fire in March, 1935.

This school remained open until the town of Lee Schools consolidated with the Rome School District in 1957. The Town of Lee demolished the building and built a new building for their town offices which were located there for many years. It is presently the site of the Lee Town Highway Department.