The airline was established and started operations on 1 October 1997. It was founded from the defunct Avianova. In March 2003 it was reported that Alitalia was considering taking over Minerva Airlines which had suspended flight operations and transferring the turboprop fleet of Alitalia Express to Minerva Airlines. This did not happen and in September 2004 Alitalia announced plans to acquire twelve additional Embraer E-170 aircraft for Alitalia Express. This did not happen, either.
In December 2008, Compagnia Aerea Italiana (CAI) took over Alitalia - Linee Aeree Italiane and Air One, merging the two companies together to create the "new Alitalia". With the take over, CAI also received Alitalia Express and Air One CityLiner. The Alitalia Express brand has been phased out and the regional arm of Alitalia is now Alitalia CityLiner by rebranding Air One CityLiner. The recent fleet of Alitalia Express (6 Embraer 170LR) was completely phased out by March 2012. Only one Airbus A320 from mainline Alitalia is now in the fleet (EI-DSC) to preserve the slots.
Alitalia Express currently has one Airbus A320 registered with Alitalia Express in order to maintain existing slots at Milan Linate Airport. Despite the fact that a plane is registered with Alitalia Express, the company is effectively closed: no plane is in Alitalia Express livery, the website is closed, and all flights with the XM code are in code-share agreement with the mainline. The aircraft assigned to work for XM is operating for Alitalia and has the Alitalia's livery.