In 1992, the predecessor airline, ValuJet Airlines, was founded by airline industry veterans, including an executive group from the former Southern Airways and pilots, mechanics and flight attendants from the defunct Eastern Air Lines. Created to fill the void at Hartsfield-Jackson Atlanta International Airport after Eastern Air Lines' demise, ValuJet Airlines started with two former Delta Air Lines' DC-9 aircraft, and the first commercial flight occurred between Atlanta and Tampa on October 26, 1993. The airline was the first to launch ticketless travel in 1993. In the spring of 1994, barely eight months after launching service between Atlanta and three Florida cities, the airline went public by listing its stock on the NASDAQ and trading under the ticker symbol VJET.

In late 1995 the airline placed an order with the then McDonnell Douglas Corporation to be the launch customer for the MD-95 aircraft (now known as the Boeing 717). Serving as the launch customer meant the airline would have significant input into the design of the aircraft, and ValuJet was the youngest airline ever to serve as a launch customer for an aircraft type. At the end of 1995, ValuJet was named as the top company in the Georgia 100 as published by the Atlanta Journal-Constitution, and the airline posted high margins with a $67 million net profit on revenues of $367 million.

The original AirTran Airways, a Boeing 737 operator with service to/from Orlando, was founded by AirTran Corporation, the holding Company of Mesaba Airlines of Minneapolis, Minnesota, operating as a Northwest Airlink carrier with hubs in Minneapolis and Detroit. In 1994, AirTran Holdings purchased a start up 737 operator named Conquest Sun and renamed the airline AirTran Airways. Conquest Sun, similar to ValuJet, was an airline started by former Eastern Air Lines employees. The original AirTran Airways moved its headquarters to Orlando, Florida, and grew to 11 Boeing 737 aircraft serving 24 cities in the East and Midwest providing low-fare leisure travel to Orlando. In 1995, AirTran Airways was spun off by Mesaba and formed its own independent holding company named Airways Corporation. On July 10, 1997, ValuJet, Inc., the holding company for ValuJet Airlines, Inc., announced plans to acquire Airways Corporation, Inc., the holding company for AirTran Airways, Inc. of Orlando, Florida. The deal was scheduled to close on November 17, 1997.

On September 24, 1997, ValuJet Airlines changed its name to AirTran Airlines. So, for a couple of months, the two holding companies, even though they had not yet merged, operated airlines with similar names – AirTran. ValuJet, Inc., operated AirTran Airlines with a hub in Atlanta and Airways, Inc., operated AirTran Airways with a hub in Orlando. Finally, on November 17, 1997, ValuJet, Inc., acquired Airways, Inc., and renamed the holding company, AirTran Holdings, Inc. In the summer of 1998, the two airlines merged onto the same FAA certificate and the AirTran Airways name survived. While the hub remained in Atlanta, the headquarters of the new entity was combined in Orlando, Florida, on January 28, 1998.

In January 1999, a new management team led by Joe Leonard, a veteran of Eastern Air Lines, and Bob Fornaro, of US Airways, took the reins at the airline. On August 15, 2001, the company's stock began trading under the ticker symbol AAI on the New York Stock Exchange. The airline grew to serve more than 56 cities coast-to-coast with more than 700 flights per day and over 9,000 Crew Members serving nearly 20 million passengers per year. In November 2007, Bob Fornaro took over as CEO, as well as President. Joe Leonard remained Chairman of the Board of Directors until June, 2008. Upon his retirement, Fornaro then became Chairman, CEO and President.

On July 1, 2003, AirTran placed an order for 100 Boeing 737 aircraft. In October 2003, AirTran began services to Washington, D.C.'s Reagan National Airport, and to San Francisco the following month. On January 5, 2004 AirTran's last Douglas DC-9 was retired, leaving it with a fleet of more than 70 Boeing 717s. The first Boeing 737 entered AirTran's fleet in June 2004, ending the service by Ryan. Later in 2004, AirTran sought a major expansion at Chicago-Midway Airport by buying the leases to ATA Airlines 14 gates. Southwest Airlines made a higher bid for the gates, and AirTran lost the deal. On May 23, 2006, AirTran accepted one of the last two Boeing 717s delivered in a ceremony with Midwest Airlines, who accepted the other 717.