Dylann Roof, 21, is alleged to have entered a Bible meeting at the American city's predominantly black Emanuel AME Church on 17 June and opened fire.
Judge JC Nicholson set a July 11, 2016, trial date and said bail, although not applied for, would be refused.
He said the accused was a flight risk - noting he was arrested in Shelby, North Carolina, the day after the shootings.
Church pastor Revd Clementa Pinckney died alongside Cynthia Hurd, 54, Revd Sharonda Coleman-Singleton, 45, Tywanza Sanders, 26, Ethel Lance, 70, Revd Depayne Middleton-Doctor, 49, Susie Jackson, 87, Revd Daniel Simmons Sr, 74 and Myra Thompson, 59.
The accused sat silent during the 25 minute hearing.