Without those charges, the Fort Worth, Texas, company posted an operating profit as it cut costs, paid less for fuel and benefited from a partnership that boosted traffic overseas.
The quarterly loss works out to 71 cents per share. A year ago, AMR lost $162 million, or 48 cents per share.
AMR Corp. said its core performance improved. It made more money per passenger and flights were fuller than any quarter before.
That effort was overshadowed late in the quarter by widespread cancellations and delays in September, which the airline blamed on its pilots.
"We haven't delivered well enough for our customers in recent weeks and our operations have certainly not been up to our high standards," Virasb Vahidi, AMR's chief commercial officer, said in an interview with The Associated Press.
Still, the airline said that costs related to the slowdown weren't material to its quarterly results.
Vahidi noted that after almost a year in bankruptcy, AMR is more than halfway to its goal of closing a gap in margins with its rivals. And unit revenue and traffic are heading in the right direction, while it's saving money from new union contracts that it signed with thousands of employees.
American also said Wednesday that 2,250 of its flight attendants took $40,000 buyout offers to leave the company. It will hire 1,500 flight attendants starting next month because such a large number accepted the buyouts.
On Tuesday, AMR asked for a 30-day extension to file a reorganization plan. It's the third time the company has asked for more time. Approval would push the deadline to late January.