The Allen University is historically significant for once being an educational institution for African Americans. It was founded in 1870, originally in Cokesbury, as the Payne Institute. From the very beginning, it was designed to educate freed black slaves.

In 1880, the Allen University was moved to the city of Columbia and was renamed as such after the honourable Bishop Richard Allen who founded the African Methodist Episcopal Church. It served as one of the only two black colleges in Columbia, allowing it to develop a strong presence in the community.

The Allen University is home to the historic Chappelle Administration Building, declared as an NHL. The campus is also a designated US Historic District and is listed on the National Register of Historic Places.