The AME Church was the first independent black denomination in the United States and was founded in 1816 in Philadelphia, Pennsylvania.

The first African Methodist Episcopal pastor in the state, William G. Steward, originally named the college Brown Theological Institute.

[1] A drawing of 1893 shows that the College President at that time was John R. Scott, Sr., first pastor of the St. Paul African Methodist Episcopal Church of Jacksonville, and a former member of the Florida Legislature.

Edward Waters was accredited as a junior college in 1955 under President William B. Stewart and five years later had a restored four-year curriculum.

In 2004, Edward Waters University had submitted documents to SACS to support their request for reaccreditation.

[4] A hearing was held in Atlanta during February 2005, and the appeal by Edward Waters University was denied.

[16] EWU competes in 16 intercollegiate varsity sports teams: baseball, basketball, cross country, football, track & field (indoor and outdoor) and volleyball; while women's sports include basketball, cross country, golf, soccer, softball, track & field (indoor and outdoor) and volleyball; and co-ed sports include competitive cheerleading.

In 2019, the university received a membership invitation to join the SIAC, a historic HBCU athletic conference playing at the NCAA Division II level.

The new facility is planned to meet NCAA specifications as part of the athletic development process associated with the move to Division II.