The unidentified child was grabbed by the alligator at 9.20pm Tuesday at the Seven Seas Lagoon on the grounds of Disney's Grand Floridian Resort and Spa, the Orange County Sheriff's Office said.
The boy's father had desperately tried to wrestle his son away from the reptile, police said.
The boy was playing in the water while his family of five, vacationing from Nebraska, relaxed on the edge of the lagoon, when he was seized by the animal, believed to be between 4 feet and 7 feet (1.2 metres and 2 metres) long, Orange County Sheriff Jerry Demings told Reuters.
A Disney spokesman said there were "no swimming" signs posted nearly.
The MailOnline reported that alligators were a common sight at the resort.
"The father entered the water and tried to grab the child and was not successful," Demings said, adding that the boy's mother also tried to rescue him and that a nearby lifeguard had also been informed of the attack.
Disney spokeswoman Jacquee Wahaler said everyone at the resort was devastated by what happened and Disney is helping the family, the Associated Press reports.
When asked if Disney was aware of alligators on the property, Wahaler advised there were signs that said "no swimming."
Demings said there had been no other recent reports of similar alligator attacks on the lake.
"We have no record of this happening before," he said.
More than 50 law enforcement officers were brought in to search for the child, including, helicopters, sonar, marine units and an alligator trapper, KTLA reports.
Wildlife and marine officials have also been drafted into the search, which will run into the night. "We are putting every effort forward," said Chad Weber, an officer of the Florida Fish and Wildlife Conservation Commission.
The tragedy comes two days after a gunman killed 49 people at a gay nightclub nearby in the deadliest shooting in modern US history.