Under the penalty, JetBlue must pay $1 million to the U.S. Treasury and use the remaining $1 million to compensate impacted passengers, the DOT says. Customers will receive at least $75 if they experience any future JetBlue delays of three hours or more within the next year.

"Today's action puts the entire airline industry on notice that we expect their flight schedules to reflect reality..."

JetBlue has agreed to pay $2 million after federal regulators charged the U.S. airline with operating multiple chronically delayed flight routes, marking the first time the Department of Transportation fined an air carrier over its scheduling practices.