Dylann Roof is accused of carrying out a shooting which killed nine people at the Emanuel African Episcopal Church on Thursday.
Roof stood quietly through the hearing, providing provided the judge with his name and address and saying he was unemployed.
Roof has been charged with nine counts of murder and possession of a firearm in connection with a church shooting in the US.
In a post on its Twitter account, Charleston Police said Roof (21) will have a bond hearing later on Friday, although he is not expected to attend.
Reports have claimed he has confessed to killing nine members of a Bible study group at the historic Emanuel Africa Methodist Episcopal church in South Carolina.
Roof was arrested on Thursday four hours from Charleston in Shelby, North Carolina.
It comes after a Snapchat by the youngest victim of the shooting - Tywanza Sanders (26) - showed a white male sat among black people at the church before the fatal shootings took place.
One of Mr Sanders' friends told Mashable: "I didn't notice until now that Dylann was just a few people away from Wanza."
"You can slightly see him in the right corner of the screenshot."
Roof is reported to have been in the prayer group meeting for an hour before allegedly opening fire.
A survivor of the attack has said the gunman reloaded five times and when asked to stop shooting, replied: "I have to do it. You rape our women and you are taking over the country. And you have to go."
"He's got to pay for this"
The other victims of the shooting have been identified as Reverend Clementa Pinckney; Cynthia Hurd (54); Reverend Sharonda Coleman-Singleton (45); Myra Thompson (59); Ethel Lance (70); Susie Jackson (87); Reverend Daniel Simmons Sr (74) and Reverend DePayne Middleton-Doctor (49).
Speaking to the Reuters news agency, the suspect's uncle, Carson Cowles, said Roof's father gave him a .45-calibre pistol in April.
Mr Cowles, who recognised Roof in a photograph released by police, described his nephew as quiet and softly-spoken.
He recalled telling his sister, the suspect's mother, several years ago that he was worried about Roof and that the boy was too introverted.
"I said he was like 19-years-old, he still didn't have a job, a driver's licence or anything like that, and he just stayed in his room a lot of the time," Mr Cowles said.
He said he tried to "mentor" his nephew, adding: "He didn't like that, and me and him kind of drifted apart."
Speaking shortly before Roof's arrest, Mr Cowles said: "Nobody in my family had seen anything like this coming. If it is him, and when they catch him, he's got to pay for this."
Local court records show Roof was charged with a drugs offence in March. He was also charged with trespassing in April.
A photograph on his Facebook page shows him dressed in a jacket adorned with the flags of Apartheid South Africa and Rhodesia.