Another 6,300 flights had been delayed by early evening, according to tracking service FlightAware.
It was the second straight day of major disruptions and the worst day for cancellations since mid-June.
The three major airports in the New York City area and Reagan National Airport outside Washington, D.C., recorded the most cancellations.
American Airlines scrubbed about 250 flights, or 7% of its schedule. Republic Airways, which operates smaller planes for American Eagle, Delta Connection and United Express, canceled a similar number, about 25% of its flights.