Delta said it takes the incident "very seriously" and is working with authorities.
The boy traveled Thursday on flight 1651, a Boeing 757 from Minneapolis to Las Vegas.
The airline spells out its policy on children flying solo plainly on its website.
Kids between the ages of 5 and 14 may travel alone as part of the unaccompanied minor program. Someone from Delta pays special attention to the children, walks them on board, shows them their seats and even introduces them to the cockpit crew, time permitting, Delta says, adding, "kids love this part."
Airport officials reviewed security footage and don't think the child had a ticket, CNN affiliate KARE reported.
The boy spent a good amount of time at the airport before boarding the plane, KARE said.
He was there the day before, the station reported, citing airport officials. He passed his time by taking luggage from a carousel, bringing it to an airport eatery and then ditching it, asking a server to watch the bag "while he went to the restroom."
Yet the potential red flags of a 9-year-old, traveling alone and leaving unattended luggage, failed to trigger any action.
The following day the child took the train to the airport, cleared security and nearly made it to Las Vegas without detection.
"Obviously, the fact that the child's actions weren't detected until he was in flight is concerning," [Patrick Hogan, a spokesman for Minneapolis-St. Paul International Airport], wrote. Still, 33 million people travel through Minneapolis' airport every year, he noted. "I don't know of another instance in my 13 years at the airport in which anything similar has happened," he said.
Image: Airplane, via Shutterstock