CityFlyer Express can be traced back to the formation of Connectair in 1983. Connectair became a feeder airline for British Caledonian, when it commenced a regional scheduled service between Gatwick and Antwerp with a single, leased Embraer EMB 110 Bandeirante turboprop on 30 May 1984. Following British Airways' takeover of British Caledonian in December 1987, Connectair operated its flights under the UK flag carrier's BA designator without adopting the British Airways livery for an interim period.
In June 1988 the firm was acquired by the International Leisure Group (ILG), the parent company of Air Europe. Following ILG's acquisition of Connectair, the airline was re-branded Air Europe Express and adopted a new corporate identity as of 1 February 1989. Air Europe Express was forced to halt its operations on 8 March 1991 along with its sister airlines in the ILG-controlled Airlines of Europe group as a result of its parent company's decision to put all the group's companies into administrative receivership on that day, even though Air Europe Express itself had remained profitable throughout that period.
The management of Air Europe Express quickly started a new airline, Euroworld Airways, and began operations in May 1991 using two Shorts 360 aircraft and staff from the old Air Europe Express. The airline rebranded as CityFlyer Express in 1992.
Meanwhile, the code share agreement with BA had resulted in several complaints being lodged with British Airways by customers expecting a BA flight and the BA product. BA proposed a solution to this by offering CityFlyer Express a franchise agreement, which it accepted. This occasion marked the conclusion of the first-ever franchise agreement between British Airways and another airline. It also marked the conclusion of the first franchise agreement in the UK airline industry. Under this arrangement the CityFlyer Express aircraft would be painted in full BA livery with interiors and cabin layout conforming to BA's contemporary, standard two-class European product. Staff would wear BA uniforms and all flights would operate under BA flight numbers. British Airways itself would take over CityFlyer's marketing and handle all reservations on its behalf. To all intents and purposes, CityFlyer Express would present itself and trade as British Airways. The deal came into effect in June 1993.
CityFlyer Express was sold to British Airways 1999 after decision of the Competition Commission, despite a higher bid of Virgin. However, a ceiling was imposed on the BA and CityFlyer Express slots at Gatwick.
British Airways' sale of BA Connect to flybe in 2007 did not include the London City Airport operations and its associated fleet of ten Avro RJ100 regional jet aircraft. This led to British Airways' decision to resurrect erstwhile Gatwick-based CityFlyer Express as a new wholly owned subsidiary BA CityFlyer to take over this operation, as of March 2007.