| The American Baptist Home Mission Society founded the school in 1865 shortly after Union troops took control of Richmond, Virginia, at the end of the American Civil War. Approximately 4 million former African American slaves, or freedmen, were to become citizens, although many had been deprived of formal education and prevented from becoming literate by Southern state laws. Southern states were in upheaval after the war. Both planters and freedmen were trying to figure out what a free labor market would entail.
Members of the American Baptist Home Mission Society (ABHMS) proposed a "National Theological Institute" to educate freedmen wishing to enter the Baptist ministry.Soon, the proposed mission was expanded to offer courses and programs at college, high school and even preparatory levels, to both men and women. This effort was the beginning of Virginia Union University.
Separate branches of the National Theological Institute were set up in Washington, D.C. and Richmond, Virginia, with classes beginning in 1867. In Washington, the school became known as Wayland Seminary, named in commemoration of Dr. Francis Wayland, former president of Brown University and a leader in the anti-slavery struggle. The first and only president was Dr. George Mellen Prentiss King, who administered Wayland for thirty years (1867–97). Famous students there included Dr. Booker T. Washington and Dr. Adam Clayton Powell, Sr.
In Richmond, the efforts were more difficult. Beginning in 1867, Colver Institute, a VUU predecessor school, was housed in a building long known as Lumpkin's Jail, a former "slave jail" owned by Mrs. Mary Ann Lumpkin, the African-American widow of the deceased white owner. In 1899, the Richmond Theological Institute (formerly Colver Institute) joined with Wayland Seminary of Washington, D.C. to form Virginia Union University at Richmond.
In 1932, the women's college Hartshorn Memorial College, established in Richmond, Virginia in 1883, became a part of Virginia Union University. Storer College, an historically black Baptist college in West Virginia (founded in 1867), merged its endowment with Virginia Union in 1964.