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The history of Benjamin Banneker Elementary school began in the social reform movement of the early twentieth century. The Original Banneker Elementary School was built in 1858 on West Street. This school served African American students in Milford. This school was used from 1858 until 1921. The philanthropist, Pierre Samuel DuPont, who was devoted to improving education, established a fund to improve existing schools and to construct new schools throughout Delaware.

In 1920, the Delaware School Auxiliary Association used funds donated by Mr. DuPont to purchase land and construct a brick building on the corner of North and Church Streets. The school opened in September 1921 as Milford School #3. The school had five classrooms for eight grade and five teachers. Mr. J. Graham Scott, the first principal of the school, also taught grades 7 and 8.

The building was enlarged in 1935 by the State Board of Education to provide home economics and industrial arts classes. Over the years, more land was purchased, and additions included classrooms, gymnasium, cafeteria, library, and science room.

In 1941, the school principal, Mr. Eldridge J. Waters, established a committee to determine a new name for the school that would recognize a great African American. The school was renamed Benjamin Banneker Elementary School in honor of the distinguished scientist and mathematician.

By 1945, Benjamin Banneker School included a junior high school and provided classes through the tenth grade. The upper grades were eventually housed elsewhere. The school continued to thrive in a community which nurtured its children and enthusiastically supported its school programs. When the school closed its doors for the 2003 summer vacation, the building was the oldest elementary school still in use in the state of Delaware.

August 25, 2003, was a new beginning for Benjamin Banneker Elementary School. The school year began in a new building with state-of-the-art facilities designed to take advantage of current computer technology. The new school building includes bright, spacious classrooms, new furniture, and a new security system. The school community is enthusiastic about the new building which honors the love of learning and spirit of inquiry of the great thinker for which it is named.