The Neos logo used until 2004 when the company was affiliated with TUI.
Neos was established on 22 June 2001 as a joint venture between Alpitour and German tour operator TUI. Revenue flights were launched on 8 March 2002. In January 2004 the TUI shares were sold to Alpitour, so that Neos is fully owned by them, except for 0.01 percent of the shares that are held by Welcome Travel. At March 2007, the company had 330 employees.
On November 19, 2012, Neos Flight 731 suffered turbulence during a flight from Holguin, Cuba, to Milan Malpensa airport. 66 passengers sustained minor injuries during the flight, carried on a Boeing 767-300.