In addition to the accolade, the airline finished second in the overall list of 17 carriers, which was topped by Honolulu-based Hawaiian Airlines.
Bob Fornaro, chairman, president and chief executive officer of AirTran Airways, said that achieving the best low-cost carrier status is "a real testament to our 8,500 hard-working crew members".
"We have distinguished ourselves again this year as a high quality airline with friendly customer service and superior baggage handling, and the AQR recognized our airline’s outstanding performance," he said.
AQR came into effect in 1991 as a method for assessing airlines’ quality of service.
AirTran finished top of the list last year, while it recorded the industry’s best lost bag ratio this time around.
The airline announced earlier this month that it would introduce new flights to Portland, Maine and Harrisburg from Atlanta between June 11th and September 8th.