The airline was established on 12 December 2001 by the Thomas Cook Group to serve the Belgian holiday market, and started operations on 13 March 2002.

Until January 2004, flight tickets could only be purchased via travel agencies as part of package tours; since then individual seat reservations are also possible.

In March 2017, parent company Thomas Cook announced its intention to sell its Belgian operations to Lufthansa.

This would have led to the layoff of 40 non-flying staff members, but Dutch group SHS Aviation announced it would take over the flight licences, two of the three remaining aircraft,[1] and the remaining 40 employees, and integrate them into a new airline, confusingly called "VLM Airlines" though no longer connected to the Antwerp VLM Airlines (since defunct), with the remaining single Airbus A320-200 transferred elsewhere within the Thomas Cook Group.

[1] At the time of the closure, Thomas Cook Airlines Belgium was flying to 36 destinations in Cape Verde, Egypt, Morocco, Tunisia and several European countries.