Formerly on the site of the current school, Stokes Pactolus High School served the community from 1927 to 1976. After its closing, students continued to attend nearby Stokes Elementary School and Wellcome Middle School. In 1992, Stokes Elementary School opened on the current site. It originally served K-5, but community support led to adding middle school. Roscoe Locke served as the first principal of Stokes School. Other principals who have served include Harold Williams, Karla Frinsko, Steve Jones, Lenora Locklear, Joe Nelson, Jennifer Poplin, Kevin Smith, Leslie Tyson, and Jennifer James.
In 2015, Stokes School became a Leader in Me school under the leadership of Jennifer James. The Leader in Me is a whole school culture model that empowers each child to develop life and leadership skills by developing the 7 habits of highly effective people. Stokes School students and staff continue to transform the school into a place where lifelong learners and leaders are developed.