American Airlines said it has fixed its reservation system said it would be resuming flights at about 5:00 pm ET, but that delays and cancellations were likely to continue for the rest of the day.
Earlier, the FAA said that all American Airline flights had been grounded at the carrier's request as it tried to fix an outage with its reservation and booking tool.
The airline is offering reservation changes at no fee to customers following the system outage.
FlightAware CEO Daniel Baker told CNBC that the flight delays are potentially affecting more than 100,000 passengers.
"At 1 p.m. they basically stopped dispatching new flights, stopped boarding new flights, stopped allowing people to check in," Baker said. "And they've announced that they are not going to resume new flight operations until 5:00 p.m."
American Airlines, a unit of AMR, operated more than 3,300 flights a day.