Jessica Linscott and her boyfriend, Roland Dow, were taken into custody Wednesday evening at Universal Studios, U.S. marshals said.
"I find it very sad that these two were located in an area designed to bring joy and happiness to children," U.S. Marshal David L. Cargill Jr. said.
Linscott, 23, and Dow, 27, had been on the run for two weeks after arrest warrants were signed for them Nov. 13 in New Hampshire. They were wanted for allegedly causing significant head injuries and burns to Linscott's son.
Police had received a call two weeks ago from Exeter Hospital, in Exeter, N.H., where the boy was being treated. He was later taken to Children's Hospital at Dartmouth in Lebanon, N.H., where he was recovering after surgery.
Tips helped to track down the couple, Rockingham County Attorney Jim Reams said.
"We were feeling pretty confident 24 hours ago that we were going to have them soon," Reams said Wednesday.
Law enforcement officials spent "countless hours" trying to find Linscott and Dow, who are from Plaistow, N.H., a town of about 8,000 residents in Rockingham County, marshals said.
Marshals looked for the couple all day Wednesday and at the end of the day found them while a crowd was breaking up after the parade and they were headed back to the theme park's attractions area, said David Charles, deputy criminal investigator for the U.S. Marshals Service in Orlando.
"They were totally surprised," he said. "They had no clue."
Linscott is accused of failing to get medical attention for her son when he was suffering seizures from a head injury and of failing to protect him from harm. She's charged with multiple counts of child endangerment.
Dow is charged with assault. Police say he struck the boy hard enough in the head to cause traumatic brain injury. He also is accused of burning the child's fingers and wrist. Police also have charged him with multiple counts of child endangerment.
The couple had said the injuries were self-inflicted, but doctors rejected that. Police have said the boy's condition is improving but that his recovery will be long and difficult.
Linscott and Dow were in jail on Wednesday and couldn't be reached for comment by telephone.
It wasn't clear when they would face arraignment in Florida on fugitive from justice charges. If they waive extradition, they'll be immediately returned to New Hampshire.