The airline was established on 14 March 2001 and started operations on 1 June 2001. Formerly known as Atlasjet International Airlines, it was set up as a subsidiary of Öger Holdings. In 2004 ETS Group acquired a 45% stake, which was increased to 90% in February 2006 following the taking over of Öger's 45% holding. The company is led by its CEO Orhan Coşkun had 730 employees (as of 2007).
In August 2012, Atlastjet Airlines contracted Ryan International Airlines, a US airline, to operate religious pilgrimage flights to cities such as Medina and Tel Aviv. In January 2013 Atlasjet failed to fulfill the payments to Ryan International, which propted the termination of the co-operation without advance notice. Ryan International Airlines, already in a bankruptcy reorganization process, was not able to recover from the loss and therefore faced impending financial difficulties, which led to its liquidation.
On 18 August 2007, Atlasjet Flight 1011 from Ercan, Northern Cyprus to Istanbul, Turkey, which was operated by a McDonnell Douglas MD-83 (registered TC-AKN), was hijacked by two passengers shortly after take-off. The perpetrators claimed to be members of Al Quaeda carrying explosives, and demanded the pilots to divert to Tehran, Iran. Instead, the aircraft landed at Antalya Airport in Turkey at 08:15 local time, officially in order to refuel. Negotiations with the local authorities began, during which all females and children on board were allowed to leave. A ruckus occurred when other passengers and crew tried to flee during which the hijackers surrendered. There were no notable injuries among the 138 other passengers and 5 crew members on board.