In 1867 John Storer, a Maine philanthropist, became interested in Reverend Brackett's school. He offered a $10,000  grant to the Freewill Baptists for a "colored school" in the south. Storer would only give the grant if his conditions were met. First he said that the school must become a degree-granting college. He also said that no applicants can be turned down because of race or sex. The last condition was that the $10,000  donation had to be met within the year.

Many residents of Harpers Ferry did not like the school. They tried everything to shut down the school. One teacher wrote, "It is unusual for me to go to the post office without being hooted at, and twice I have been stoned on the streets at noonday". The peoples' efforts did not succeed: Storer College was not closed.

The college existed as place where blacks could achieve an education in spite of the Jim Crow laws of the segregated South. Oddly, the college's fate was the same as the segregationist policies that gave rise to its existence. In 1955 Storer College closed its doors forever. This was a result of the Supreme Court decision on Brown v. Board of Education. The decision ended legal segregation in public schools. When this happened West Virginia no longer supported the college financially.