The town of Lincoln, originally called Goose Creek, was populated largely by Quaker farmers who were concerned with the religious training and education of their children. The Quaker community set aside ten acres of land in 1757, some of which was dedicated  for a one room log schoolhouse. 

In 1815, the Oakdale School was built by contributions from community families. It was also a one room school, but made out of bricks. Oakdale School was open to all the community children, regardless of faith or wealth. Students studied penmanship, spelling, reading and arithmetic. Geography was introduced at  about twelve years of age; grammar at fourteen. School was held all year long, with the exception of two weeks during the wheat harvest. In winter, about seventy students attended regularly. There were fewer students in summer, when they were needed to work on the farms.

A new school was built in 1880 a short distance from the Oakdale School. This was a two story brick building. The first floor was a large, single room for the elementary students and was again paid for by donations from local families. The second floor was also one large room, but was funded by the Commonwealth of Virginia for high school students. It was called Lincoln School, and was the first high school in Loudoun County.

When Lincoln School became overcrowded, some elementary students moved to the Oakdale School building until another new school opened in November 1909 at the present site  of Lincoln Elementary School. This school was very well equipped for the time, with a chemistry lab, tennis and basketball courts and athletic fields. To attract  excellent teachers, the community provided funds to pay higher salaries than other nearby schools. High school and elementary students attended this new school together until overcrowding again became an issue. 

In 1916, the old Lincoln School was remodeled and elementary students returned there.On April Fools Day 1926, the high school building burned. A one story brick building was built on the site and and was ready for students to attend the next school year. High school students remained in this building until 1955, when the new Loudoun County High School opened. The Lincoln High School became Lincoln Elementary School. 

In 1974 the first cottage was built to provide space for kindergarten classes, and in 1989 another cottage was added to become the fifth grade classroom.