The man was taken into custody after crew members intervened, American Airlines said.
The passenger ran down the jetway and into the cockpit of the Boeing 737-800, which was carrying 121 passengers and six crew members.
He damaged flight controls and attempted to jump out of an open window as pilots tried to stop him, ABC News reported.
The man was not immediately identified. There were no reports of injury.
"We applaud our outstanding crew members for their professionalism in handling a difficult situation," American Airlines said.
The damaged aircraft was grounded at Ramon Villeda Morales International Airport in San Pedro Sula, Honduras, the airline said.