The incident happened last month at Chicago's Midway Airport. There were 85 passengers and crew on board the Southwest plane.
An NTSB report shows the Boeing 737 just landed at Midway on Dec. 1and was cleared to cross another runway when the first officer yelled for the captain to stop.
"We just had a plane take off 31 right, you cleared us to cross," the Southwest pilot said to the controller. "You cleared us onto a runway. There was a plane taking off."
The captain stopped short of the runway edge as a Learjet took off a mere 287 feet above and 62 feet in front of the larger plane.
Things quickly got tense.
"You got a phone number to call you?" the pilot said.
"Yes we do," the tower responded.
"I want to acknowledge you cleared us to cross a runway. A plane was taking off," the pilot said.
"Contact ground please," the controller said.
Prior to the incident, air traffic controllers did not cancel the takeoff clearance of the Learjet, nor tell the Southwest plane to hold short of the runway, according to the report.
"Be advised, tower sent us across 31 right, and a Learjet of some sort was taking off, and we had to hit the brakes, and the thing went right over our head," the pilot said.
No one on either plane was injured. Southwest Airlines says it is cooperating with federal officials investigating the incident.
"I don't think people should be nervous. Certainly we've got an incredible record over the last 10 years," said John Nancy, ABC News aviation consultant. "But I do think that the rising drumbeat of these incidents means that the FAA is going to have to look very carefully at the work-rest plan especially and the number of controllers on duty."