Gary Holmes, 33, faces capital murder and terroristic act charges in connection with the shooting, Pulaski County Sheriff's Office spokesman Lt. Cody Burk said.
The arrest came almost a week after Acen King was shot dead in the back seat of his grandmother's car.
Holmes turned himself in Thursday night, police said. He was arraigned Friday morning in Little Rock District Court and pleaded not guilty. He was ordered held without bond.
The shooting sparked a community outcry
and police had offered a $40,000 reward for information leading to an arrest and conviction in the case.
Police said Friday they received a tip that Holmes had been in his girlfriend's black Impala. She told police he was driving the car Saturday and had a semi-automatic pistol in his lap. He became angry because he thought a car behind him was following too closely, and he pulled over to let the car pass.
The car then stopped at a stop sign for a "few minutes," the woman reportedly told police. Holmes honked, got out of the car and fired a single shot into the other car.
Acen was in the back seat with his 1-year-old brother. Their grandmother said she was unaware the car was hit and she drove on to a J.C. Penney about nine miles away. There she noticed Acen was hurt and called 911.
The grandmother told police the incident began when a man in a car behind her at a stop sign started honking his horn, apparently upset she wasn't moving quickly enough. The grandmother honked her horn, too.
"One shot was fired, and it went through the vehicle and hit the child," said Lt. Steven McClanahan, Little Rock police spokesman.
"She didn't know he was shot," a bystander told the 911 operator after speaking with the grandmother. One of the callers, describing to the 911 operator what happened, said the grandmother feverishly performed CPR after the child sustained a neck wound.
The boy was transferred to Arkansas Children's Hospital, where he was pronounced dead. The other child was not wounded, according to the police report.
Police said they believe the grandmother and the slain boy had no relationship with the gunman.