The charge, which will also affect American Eagle passengers, will apply to travelers who purchase domestic economy-class tickets on or after May 12, the airline said.
The move comes after recent similar policy changes at Continental Airlines, Alaska Airlines, United Airlines and Northwest Airlines.
The company's AAdvantage Gold, AAdvantage Platinum and AAdvantage Executive Platinum frequent flyers are exempt from the charge.
The policy also does not apply to full-fare economy, business and first-class tickets, or international trips excluding Canada and U.S. territories.
Based on those exceptions, American said it expects about 4 percent of its domestic customers who check more than one bag will be charged the $25 second-bag fee.
Shares of AMR Corp., American's parent company, were unchanged in early trading.