FAA chief Randy Babbitt said in a statement that he has accepted Hank Krakowski's resignation.
"Hank is a dedicated aviation professional, and I thank him for his service," Babbitt said in the statement.
Babbitt said David Grizzle, FAA's chief counsel, will temporarily take over for Krakowski while the agency searches for a replacement.
On Wednesday, the FAA announced that a second air traffic controller will be staffed on the midnight shift effective immediately at 27 control towers in the U.S. Among the facilities that have an extra set of eyes are Bob Hope and ontario airports.
The controllers were added hours after a lone controller fell asleep while a medical flight was trying to land at 2 a.m. at Reno-Tahoe International Airport.
It was the latest in a string of incidents of sleepy controllers. There have also been incidents at Washington's Reagan National Airport, McGhee Tyson Airport in Knoxville, Tenn, Boeing field in Seattle and an airport in Lubbock, Tx.
Babbitt said he would conduct a "top to bottom" review of FAA's entire air traffic system.
"Over the last few weeks we have seen examples of unprofessional conduct on the part of a few individuals that have rightly caused the traveling public to question our ability to ensure their safety," Babbitt said. "This conduct must stop immediately."
FAA officials will meet privately on Thursday with members of the House Transportation and Infrastructure Committee, which oversees FAA's budget. Key members of Congress - including Senate Majority Leader Harry Reid, D-Nev., and Sen. Jay Rockefeller, D-W.Va. - have demanded FAA stop controllers from sleeping on the job.
The National Air Traffic Controllers Association, the union that represents the FAA's 15,000 controllers, plans to visit airports across the country next week.
The Associated Press contributed to this report.