A senior government official said the man first told a member of the cabin crew that he was going to blow up the plane as it was preparing to take off from Amman's Queen Alia International Airport en route to Dubai.
The man was then arrested without a struggle, the official said, and bomb squads searched the plane and found nothing.
"Luckily, it was a false alarm," he said, on condition of anonymity because he was not authorized to speak to the press.
The man later told authorities that he "was joking," according to police and the government official.
The man said he worked as a co-pilot for a private aviation firm in Dubai, police added.
"He insisted to one of the cabin crew members on entering the cockpit, to speak with the pilot," the government official said, and when the flight attendant refused, he "claimed he had a grenade and he would use it to blow up the plane."
The flight, from the low cast carrier flydubai, was delayed for three hours due to the incident.
The man, who was not identified, is under investigation and will be prosecuted, said police.