The company holds a United Kingdom Civil Aviation Authority Type A Operating Licence permitting it to carry passengers, cargo and mail on aircraft with 20 or more seats.

Flybe started operations on 1 November 1979 as Jersey European Airways (JEA), after taking over the operations of Intra Airways. Jersey European Airways was the brainchild of John Habin, a resident of Jersey and the majority investor in JEA. Having sold Aviation Beauport and other business interests, Habin established a few key routes from Jersey to the UK. Jersey European Airways was taken over in 1983 by Jack Walker's Walker Steel Group who were already the parent company of Blackpool based charter airline Spacegrand Aviation. The two airlines were run separately, with partially shared management, until their amalgamation within the Walker Aviation Group in 1985, under the Jersey European name.

The airline rebranded as British European in June 2000, shortening this title to Flybe on 18 July 2002 and repositioning itself as a full service, low-fare airline. On 3 November 2006 it was announced that agreement in principle had been reached for Flybe to acquire BA Connect, with the exception of London City Airport services. The acquisition was completed in March 2007. The airline is owned by Rosedale Aviation Holdings (69%), Flybe staff (16%) and British Airways (15%) as a consequence of the acquisition of BA Connect. It had 3,000 employees at January 2008. As per the CAA's April/May 2009 passenger statistics, Flybe is now the UK's largest domestic airline (26% of total UK domestic passengers that flew during April chose a Flybe-branded flight, 3% more than those who chose an easyJet-branded flight). It carried 451,413 domestic passengers during April 2009, excluding franchise flights operated by Loganair. This puts Flybe in pole position among the UK's domestic carriers, ahead of easyJet, British Airways, the BMI Group and Ryanair. During that period Flybe also became London Gatwick's leading domestic operator. Chief Executive Officer Jim French was recognised in the 2009 Queens' Birthday Honours’ List with a CBE for his services to the UK airline industry.

On 5 March 2007 Flybe completed the acquisition of the former regional airline business of British Airways. The purchase was first announced on 3 November 2006 with British Airways acquiring a 15% stake in the airline. The acquisition (which did not include BA Connect's London City Airport routes, which have been taken over by BA CityFlyer) has increased Flybe's route network in both the UK and continental Europe making Flybe Europe's largest regional airline.

On 14 January 2008 it was announced that Flybe had signed a franchise agreement with Scottish airline Loganair, to commence on 26 October 2008 following the termination of Loganair's franchise agreement with British Airways on 25 October 2008.

The agreement will see Loganair aircraft flying in Flybe colours on 55 routes from Scotland.

Flybe operates short haul services to destinations throughout the United Kingdom, Ireland and continental Europe.

Flybe (2002-present)

Jersey European (1991-2000)

As of July 2010, the Flybe fleet includes the following aircraft: