Bowie State University is an outgrowth of the first school opened in Baltimore, Md. by the Baltimore Association for the Moral and Educational Improvement of Colored People, which was organized on December 15, 1864 to engage in its self-appointed mission of offering educational opportunities that the state failed to provide for its Black citizens.  The first school, offering courses in the elements of education, was opened on January 9, 1865 in the African Baptist Church located on the corner of Calvert and Saratoga streets. The first courses in normal education to train teachers were offered at the same location in 1866. The facility was woefully inadequate to house both schools, In 1867, with the aid of a grant from the Freedmen's Bureau, the Quakers of England and others, the Baltimore Association purchased from the Society of Friends a building located at Courtland and Saratoga streets for the relocation of its normal school.

The Baltimore Normal School received occasional financial support from the City of Baltimore beginning in 1870 and from the state since 1872. In 1871, it received a legacy of $3,500 from the Nelson Wells Fund, established before Wells' death in February 1843 for the Wells Free School with the similar intent of providing for the education of freed Negro children in Maryland. On April 8, 1908, at the request of the Baltimore Normal School Board, which desired permanent status and funding as an institution for the education of Negro teachers, the state legislature authorized its Board of Education to assume control of the school. The same law re-designated the institution as Normal School No. 3. Subsequently, it was relocated on a 187-acre tract in Prince George's County in 1911 and by 1914 it was known as the Maryland Normal and Industrial School at Bowie.

A two-year professional curriculum in teacher education which started in 1925 was expanded to a three-year program in 1931. In 1935, a four-year program for the training of elementary school teachers began and the school was renamed Maryland State Teachers College at Bowie. In 1951 the college expanded its program to train teachers for junior high schools. Ten years later, a teacher-training program for secondary education was instituted. In 1963, a liberal arts program was started and the name was changed to Bowie State College.

In 1970, Bowie State College was authorized to grant its first graduate degree, the Master of Education. A significant milestone in the development of graduate studies at Bowie State was achieved with the Board of Trustees' approval of the establishment of the Adler-Dreikurs Institute of Human Relations in 1975. Currently, the University offers bachelor's and master's degree programs across a broad range of disciplines and doctoral degrees in educational leadership and computer science. On July 1, 1988, Bowie State College officially became Bowie State University, a change reflecting significant growth in the institution's programs, enrollment and service to the local area. On the same day, the University also became one of the constituent institutions of the newly formed University System of Maryland.

In 1995, Bowie State University won an 11-year $27 million award from the National Aeronautics and Space Administration/National Science Foundation to become one of only six national Model Institutions for Excellence in science, engineering and mathematics. This award significantly strengthened the institution's academic infrastructure and enhanced an already excellent computer science and technology program that continues to expand.

In 2005, Bowie State unveiled a supercomputer that had been built by faculty and students. It was the fastest supercomputer on any college campus in the state and the eighth fastest in the country. With this achievement, the University emerged as a leader among higher education institutions in computing power.

Among the nation's leaders in teacher education, with continuous accreditation by the National Council of the Accreditation of Teacher Education (NCATE) since 1954, Bowie State's legacy of producing outstanding teachers and school administrators continues to grow with recent graduates including county and state Teachers of the Year.

Today, Bowie State University enrolls a diverse student body of more than 5,400 and provides them with rigorous academic programs and the individual support they need to be prepared to compete in a changing world.