In 1993 it became the first British Airways (BA) franchisee operating as British Airways Express. CityFlyer's ownership passed to BA in 1999 when that company bought out the original promoters as well as 3i, the airline's main shareholder at the time. Initially, CityFlyer continued to operate as a separate unit, but it was eventually absorbed into British Airways' mainline short haul operation at Gatwick in 2001, the result of a change in British Airways' strategy for its Gatwick operation.

Following its absorption into British Airways, the airline's turboprops were retired, while the company's fleet of regional short-haul jetliners and the associated crews were transferred to British Airways' regional operation in Birmingham and Manchester. This in turn resulted in British Airways mainline short haul crews based at Gatwick operating most of the erstwhile CityFlyer Express routes using the former's Gatwick-based Boeing 737 fleet.

CityFlyer Express can be traced back to the formation of Connectair in 1983. Connectair became a feeder airline for British Caledonian, at the time the UK's so-called Second Force airline, on 30 May 1984 when it commenced a regional scheduled service between Gatwick and Antwerp with a single, leased Embraer EMB 110 Bandeirante turboprop. A small number of larger capacity, more efficient Shorts 330 turboprops eventually replaced the Embraer Bandeirante.

There was joint ticketing for both airlines, Connectair flight numbers were prefixed with British Caledonian's BR designator, the two-letter IATA code identifying the airline on whose behalf a flight is operated, and all of the company's aircraft were painted in the British Caledonian Commuter livery. However, this relationship stopped short of a franchise agreement.

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