"The Board is grateful for Dr. Miller’s service and commitment to LeMoyne-Owen for the past four years," Board of Trustees Chairman Christopher Davis said in a letter.
Davis said the college will name an interim president as the board discusses plans to find the next president.
Miller was the subject of a no-confidence vote in June 2017, when nearly all of the college's 51 full-time faculty members said they were dissatisfied with her leadership.
Faculty members said Miller had unfair hiring and firing methods, although Bob Simpson, then chairman of the board, called her "probably is the best thing to happen to LeMoyne-Owen in many years."
Last year, she was accused of plagiarizing part of a speech by Pastor Joel Osteen. Miller admitted she used passages from Osteen but said she did not credit him due to an oversight on her part.
"People are not really surprised. No one is saying, 'Oh my God. I hate that happened," Alumni Association President Katrina Thompson said.
Miller is the college's first female president.