SkyWest -- which partners with carriers like United, Delta, U.S. Airways, and American Airlines -- carried 27.9 million passengers in 2014.
The flight that the FAA says stalled en route from Denver to Oklahoma City rapidly descended from 39,000 feet to 27,000 feet, but managed to land without incident at its scheduled destination, according to the FAA.
With the new restrictions -- 35,000 feet for SkyWest's CRJ700 and 900 aircraft and 33,000 feet for CRJ200 aircraft -- the FAA likely hopes to give SkyWest pilots a larger margin for error.
The FAA also imposed minimum cruise speeds: approximately 272 mph for CRJ200s and approximately 288 mph for SkyWest CRJ700s and 900s.
At higher altitudes, experts say, minor mistakes can prompt jets to lose lift and stall. Slow speeds can also cause stalls.
"A stall happens when the airflow over the wing is interrupted, and basically you stop flying for a period of time," explains ABC Aviation consultant John Nance. "You have to take action immediately, and if you mishandle it you can end up in an even worse situation."
With 10,777 employees and more than 300 planes, the airline operates more than 1,800 flights each day, according to its website. Its hubs include Chicago O'Hare, Los Angles International, Denver International, and Houston International airports, among others.
The airline has not addressed whether any it plans to conduct any crew re-training.
SkyWest called the FAA's decision "a head-scratcher," saying their their plane didn't stall, but rather experienced a "slow speed event."
"Months ago, one SkyWest CRJ aircraft experienced an isolated slow speed event, which is when an aircraft reaches less than optimal speeds. The aircraft's slow speed alert systems functioned perfectly, and the crew responded appropriately with a 4,000-foot descent. No stall occurred," SkyWest said in a statement to ABC.
The airline called the FAA's decision "a sweeping and arbitrary reaction that was not fully explained."
"We expect that when the FAA fully analyzes the data, it will lift all restrictions," the arline continued. "SkyWest is an industry leader in safety and is committed to ensuring each of our flights operates safely."