British Airways' sale of BA Connect to Flybe in 2007 did not include the London City Airport operation and its associated fleet of ten Avro RJ100 regional jet aircraft. This led to BA's decision to resurrect erstwhile Gatwick-based CityFlyer Express, which it had integrated into its Gatwick mainline short-haul operation in 2001 following that airline's acquisition in 1999, as a new wholly owned subsidiary to take over this operation as of March 2007. BA CityFlyer was awarded an Air Operators Certificate on 8 February 2007 and started operations on 25 March 2007.
Prior to 2009, BA CityFlyer operated a fleet of Avro RJ85 and Avro RJ100 aircraft. In December 2008 the airline signed a contract with Embraer to modernise the fleet with an order for 11 E-Jet aircraft, comprising 6 Embraer E-170s and 5 Embraer E-190s, deliveries of which commenced in September 2009. On 14 July 2010, BA CityFlyer operated the last revenue sector with a RJ85.
BA CityFlyer announced an order of 3 extra Embraer 190 aircraft on the 15th November 2013. 
On 13 February 2009, BA CityFlyer Flight 8456, an Avro RJ100, registered G-BXAR, flying from Amsterdam suffered a nose-gear collapse whilst landing at London City Airport. None of the 67 passengers or 5 crew members were seriously injured in the incident, but 2 passengers were sent to hospital, one of whom suffered minor injuries. After a normal approach and touchdown, the nose landing gear fractured due to the presence of a fatigue crack in the upper internal bore of the landing gear main fitting. The crack had formed as a result of poor surface finish during manufacture and the incomplete embodiment of a manufacturer's service bulletin which the landing gear maintenance records showed as being implemented at its last overhaul in June 2006. The aircraft was damaged beyond economic repair and was written off by insurers in May 2009.