Chief executive Craig Kreeger said weak economic conditions and the Olympic Games in London, which dented demand for business travel, were factors in the airline's latest loss of £93 million for the year to February 28.
It has also suffered from high fuel costs, strong competition on transatlantic routes and taxes on UK air travel, although the figures showed it still increased revenues by 5% to £2.9 billion. It carried 5.5 million passengers in the period, an increase of 188,000 on a year earlier.
Mr Kreeger, who took over from Steve Ridgway as chief executive in February after a 27-year career at American Airlines, recently announced a staff pay freeze as part of a wider cost-cutting programme.
He said: "I am confident we have concrete plans in place to take Virgin Atlantic forward and return the business to profitability within a two-year frame."
Virgin hopes that its ties with US operator Delta, which acquired a 49% stake in the airline last year, will help it compete more forcefully with the British Airways-American Airlines alliance in the lucrative transatlantic market.
The latest loss contributed to a pre-tax deficit of £69.9 million for the wider group, which includes Virgin Holidays. The previous year's group loss was £80.2 million, with the airline deficit being £98.6 million in 2012.