Virgin Atlantic’s UK domestic arm Virgin Little Red ceased operations over the weekend.
The final flights between Heathrow and Edinburgh and Aberdeen using leased Aer Lingus aircraft ceased on Saturday.
A service between Manchester and London was withdrawn in March.
Little Red was established in March 2013 in an attempt to provide more competition on domestic routes following the takeover of BMI by British Airways.
But the domestic offshoot failed to provide the connecting traffic Virgin Atlantic had hoped for.
The withdrawal has raised concerns in Scotland over BA retaining a monopoly on Scottish routes to Heathrow despite competition from easyJet, Ryanair and Flybe to other London airports.
The closure of Little Red was announced last October with chief executive Craig Kreeger admitting then that the time lag between the takeover of BMI and Little Red entering the market meant the short-haul offshoot initially faced an “uphill battle to win recognition and convert customers to its services”.
He added: “While this challenged environment meant Little Red ultimately did not deliver the results we had hoped, this certainly will not dampen our enthusiasm to try new things in the future.”