British Midland Regional Limited, which operated as flybmi, announced on Saturday evening that it was filing for administration.
It is understood 1,500 passengers had been scheduled to fly with the airline on Sunday.
A total of 376 employees based in the UK, Germany, Sweden and Belgium are employed by bmi Regional.
The East Midlands-based airline had operated flights on routes to 25 European cities, including Aberdeen, Bristol, City of Derry, East Midlands, London Stansted and Newcastle.
It was claimed some passengers were still able to make bookings on Saturday, hours before the announcement of the collapse came.
A tweet from the airline a day earlier invited people to book a trip with flybmi to Munich for winter sports.
Rory Boland, travel editor at Which?, said: “Some customers have claimed that tickets were being sold in the hours before the airline went bust, knowing full well those tickets would never be honoured, and passengers will rightly be outraged if this is proved to be the case.”
In a statement, the airline said difficulties which led to the collapse had included increases in fuel and carbon costs, and challenges “particularly those created by Brexit”.
A statement on its website said: “The airline has faced several difficulties, including recent spikes in fuel and carbon costs, the latter arising from the EU’s recent decision to exclude UK airlines from full participation in the Emissions Trading Scheme. These issues have undermined efforts to move the airline into profit.
“Current trading and future prospects have also been seriously affected by the uncertainty created by the Brexit process, which has led to our inability to secure valuable flying contracts in Europe and lack of confidence around bmi’s ability to continue flying between destinations in Europe.
“Additionally, our situation mirrors wider difficulties in the regional airline industry which have been well documented.
“Against this background, it has become impossible for the airline’s shareholders to continue their extensive programme of funding into the business, despite investment totalling over £40 million in the last six years.
“We sincerely regret that this course of action has become the only option open to us, but the challenges, particularly those created by Brexit, have proven to be insurmountable.”
Customers have been advised to contact their payment card issuer to get a refund for flights, while those who have booked through a travel agent or partner airlines are advised to contact their agent or airline for details of their options.
One passenger said he had already gone through security at Bristol airport when his flight was cancelled, while another said their planned flight this Tuesday was “up the swanny then”, adding: “Charity event to be revisited as and when I get official word”.
Civil engineer Danny McLaughlin, who lives along the Irish border, said it is the first direct effect of Brexit he has felt.
The 46-year-old father-of-two, who lives near Buncrana in Co Donegal, had 14 flights booked through his job over the next seven weeks between City of Derry Airport and London Stansted.
He said: “I’m a bit stunned to be honest with you. I know airlines and things have been saying this for quite a while but it just came as a bolt out of the blue.”
Just two days earlier, Transport Secretary Chris Grayling had announced the route between City of Derry Airport and London Stansted would be subsidised by the Government, in partnership with the Department for the Economy in Northern Ireland for another two years until May 1, 2021.
Discussions are now under way to find an airline to operate the route, which is a public service obligation.
A DfT spokesman said: “It is very disappointing that flybmi has gone into administration and we know this will be a very difficult time for those who have lost their jobs as a result.
“This will also of course be disruptive for passengers. We are fully focused on supporting those affected and are in contact with airports, airlines and other transport providers to ensure everything possible is being done to help them.”
Brian Strutton, general secretary of the British Airline Pilots’ Association (Balpa), said: “The collapse of flybmi is devastating news for all employees.
“Regrettably Balpa had no warning or any information from the company at all.
“Our immediate steps will be to support flybmi pilots and explore with the directors and administrators whether their jobs can be saved.”
In December, flybmi announced plans to launch a daily service between Leeds Bradford Airport and the home of Oktoberfest.
The new route to Munich in Germany would have given business and leisure travellers a link to Bavaria’s capital city - a key business destination and a cultural hot spot.