The teenager was unharmed despite frigid temperatures at 38,000 feet and a lack of oxygen.
FBI spokesman Tom Simon said the boy was questioned after being discovered on the tarmac at the Maui airport with no identification.
Mr Simon said security footage from San José airport verified that the boy hopped over a fence to get to Hawaiian Airlines Flight 45 on Sunday morning. He said the child had run away from his family and was being referred to child protective services.
Hawaiian Airlines said airline personnel noticed the boy on the ramp after the flight arrived and immediately notified airport security.
"Our primary concern now is for the wellbeing of the boy, who is exceptionally lucky to have survived," it added.
In 2012 a man died after falling on to a London street from a flight from Angola.