Atlas Air began operations in 1992. The airline's founder, Michael Chowdry, started by leasing aircraft to other airlines on an Aircraft, Crew, Maintenance, and Insurance (ACMI) contract basis. The first customer, China Airlines, contracted one airplane to start ACMI service in 1993. By 1995, Atlas Air began trading publicly and in 1997, Atlas placed an order for ten new Boeing 747-400F aircraft. Orders for another two 747-400Fs were placed in 1998.
On January 30, 2004, Atlas Air Worldwide entered Chapter 11 bankruptcy. In July 2004, the parent company completed its restructuring plan and emerged from Chapter 11 bankruptcy protection.
In March 2010, Atlas Air was awarded a nine-year contract for the operation of the Boeing 747 Large Cargo Freighter (LCF) 'Dreamlifter' for transporting aircraft parts to Boeing from suppliers around the world. It commenced operation in September 2010 under a CMI (Crew, Maintenance and Insurance) contact.
In 2011, Atlas Air took the first North American delivery of the Boeing 747-8 Freighter (Boeing 747-8F).
In September 2012, Atlas Air renewed a training contract with the United States Air Force to continue to provide training for the pilots of Air Force One. The contract also provides training for the Presidential Airlift Group for a five-year period.