The runaway managed to sneak past gate agents at multiple security stops before taking a seat on the plane.
Delta Flight 1651 left with the 9-year-old on board. It wasn't until the plane departed that the flight crew became suspicious of the child's circumstances and contacted Las Vegas police.
The boy was taken into custody upon landing and transferred to Child Protection Services.
Patrick Hogan, the Director of Public Affairs and Marketing at Minneapolis-St. Paul International Airport released the following statement to ABC News: "Obviously, the fact that the child's actions weren't detected until he was in flight is concerning. More than 33 million people travel through Minneapolis-St. Paul International Airport every year, and I don't know of another instance my 13 years at the airport in which anything similar has happened."
Video also shows the unidentified boy at the airport Wednesday, Hogan said. The boy allegedly grabbed a bag from the carousel and ordered lunch at a restaurant outside of the security checkpoints. He ate and then told the server he had to use the bathroom, left the bag and never returned to pay.
Both Delta Airlines and the Transportation Security Administration say they're investigating the incident.
TSA released the following statement Sunday: "The child was screened along with all other passengers to ensure that he was not a threat to the aircraft."
Officials say the boy was expected to return to the Twin Cities.
The Associated Press contributed to this report.