Hawaiian Airlines personnel noticed the teen on a ramp and notified security, airline spokeswoman Alison Croyle said in a statement released Sunday night.
“Our primary concern now is the well-being of the boy, who is exceptionally lucky to have survived,” the statement said.
Simon said the teen had run away from home. There was no indication that he posed a threat to the airline, and he has not been charged with a crime, officials said.
He cleared a medical checkup and was handed over to officials from the Hawaii Department of Human Services. Officials did not release his name because he is a minor.
Rosemary Barnes, a spokeswoman at the San Jose airport, said the FBI and Transportation Security Administration were investigating how the teen breached security and made it onto the plane but could provide no further comment.
The teen's case is extreme, but it's not the first time a stowaway has survived a flight in the wheel well of an aircraft.
In August 2013, a teenage boy from Nigeria endured a 35-minute trip in the wheel well of a domestic flight that landed in Lagos. Officials credited the trip's short flight time and relatively low altitude with helping him survive.
On another occasion, a stowaway managed to survive a flight from Havana to Madrid, according to the Federal Aviation Administration.
But in 2012, the body of a 26-year-old stowaway was found crumpled on a suburban London street. Officials believe he had climbed aboard a British Airways plane in Angola and was either dead or near death as he fell from the wheel well during the plane's descent into Heathrow Airport.