Carl Pistorius is charged with culpable homicide over the death of a woman motorcyclist in a traffic accident in 2008, his lawyer said.
The case has no relation to the charges against Oscar Pistorius over the shooting of Reeva Steenkamp.
The Paralympic star – who was released on bail on Friday – denies murder.
The charge against Carl Pistorius over an accident involving his car in which a woman on a motorcycle died has only just emerged.
It was confirmed to the BBC by Pistorius family lawyer Kenny Oldwage, who said Carl appeared in court the day before his brother’s judgement in the bail hearing last week.
He is due to appear again in March.
“There is no doubt that Carl is innocent and the charge will be challenged in court,” Mr Oldwage said in a statement. “Carl deeply regrets the incident.”
The accident took place in the town of Vanderbijlpark, an hour’s drive south of Johannesburg.
Police conducted tests on Carl Pistorius and he was found to have no alcohol in his blood at the time, the lawyer said.
He added that charges brought after the accident were dropped but subsequently reinstated by South African prosecutors.
Carl Pistorius was a constant presence at his brother’s four-day bail hearing.
Oscar Pistorius admits shooting Reeva Steenkamp at his home on Valentine’s Day but denies murder, saying he mistook her for an intruder.
On Sunday, a representative of the Pistorius family said they sent two bouquets of flowers to Ms Steenkamp’s family the day before her funeral.
One was from Oscar and the other from the Pistorius family and both had handwritten notes, she said.
On Saturday Ms Steenkamp’s mother June said she had received the flowers.
“But what does it mean?” she asked. “Nothing.”