After being stuck for nearly an hour, most of the passengers were able to walk to the nearest stations.
Port Authority personnel helped evacuate the passengers along walkways that run parallel to the tracks.
Shuttle bus service was provided from Jamaica Station and Howard Beach Station to Federal Circle at JFK.
The AirTrain made its inaugural run in December 2003, connecting the airport with the Long Island Rail Road and the city's subway system.
The $1.9 billion, eight-mile rail line was originally scheduled to open in 2002, but was delayed after a crash that killed a man and caused an estimated $4 million in damage.
Daily News: Outage turns JFK ride into no-wAir Train by Warren Woodberry, Jr. and Bill Hutchinson...
A mysterious power outage brought the Kennedy Airport AirTrain to a sudden stop yesterday, stranding hundreds of riders, including 30 who got stuck between stations, officials said.
The entire nine-train light rail system shut down about 9 a.m. and was powerless for at least three hours.
Diana Thomas, 51, had just flown in from her hometown of Orrville, Ohio, and was headed to visit relatives in Howard Beach, Queens, when her train stopped on the tracks well short of the Federal Circle stop. There are no drivers on the AirTrain. They are automated.
"We were on there for an hour and a half," said Thomas, explaining they had to wait until a driver could board the train and move it into the station.
Port Authority officials said another train stalled between Terminal 4 and the stop for Terminals 2 and 3. A total of 30 people were on the two stuck trains, while hundreds more were left in the lurch, waiting for the system to start up.
Officials said the cause of the snafu was under investigation. Shuttle buses replaced the AirTrain, which wasn't running again until about noon.
But Diane Lee, 57, an importer from Golden, Colo., said the wait for a shuttle bus was at least 30 minutes, barely giving her enough time to catch a 12:30p.m. flight home.
"And we got here two hours early," said Lee, who had her bags misplaced on her way to New York last week.
The last time a systemwide failure shut down the 8.1-mile loop AirTrain track was in October 2005.