The firm is offering an exclusive discount of 30% off advance fares to areas affected by the flooding as part of a three-month promotion starting next week.
Virgin has teamed up with VisitEngland to boost tourism and support the #Openforbusiness message in Cumbria, Yorkshire, Lancashire and Northumberland.
The partnership comes four days after the government’s announcement of the Flood Recovery Fund and a new £1m ‘Staycation’ marketing campaign to promote tourism in the North of England.
Culture secretary, John Whittingdale, said: "I very much welcome this initiative by Virgin Trains which will encourage even more people to visit the North and see its stunning countryside, vibrant cities and world-class attractions.
“The government is actively supporting our tourism businesses as they recover from the recent floods and showing that the area is open for business.
“This new deal will encourage many more people to enjoy a break in the North over the coming weeks.”
Virgin aims to boost visitor numbers following the damage caused by storms Desmond, Eva and Frank in December. The offer is timed to coincide with the February half-term holiday and Easter break in March.
Discounted fares are available as of 9 Feb on direct services to destinations including Carlisle, Lancaster, Oxenholme, Penrith and Preston on the west coast route and Berwick-upon-Tweed, Doncaster, Leeds, Morpeth and York on the east coast.
These fares will be available three weeks before the date of travel.