Details of the domestic programme have been revealed three weeks after Sir Richard Branson's airline won the right to go head-to-head with its old rival British Airways by taking up slots used by BMI.
It will fly six return trips a day to Edinburgh and three to Aberdeen, with a further six return flights to Manchester, which will be launched on March 31. A total of 150 jobs will be created, 24 in Aberdeen and Manchester and the remainder at Heathrow, the airline said.
However, the schedule will not include Glasgow Airport, whose management had lobbied the airline after complaining that it has not been included in action by the European Commission to promote competition on routes between Scotland and Heathrow.
British Airways, whose parent company IAG purchased the loss-making BMI from Lufthansa earlier this year, was forced by the European Commission to hand over a number of Heathrow landing slots to ensure the deal did not weaken competition.
It is currently the sole operator of services to Heathrow at Edinburgh, Aberdeen and Glasgow. However, Glasgow was not protected by the European Commission's actions as BMI pulled out of the route in March last year, before the deal was done.
A ruling by the European Commission found British Airways had been able to significantly increase fares between Heathrow and Glasgow and Heathrow after BMI pulled out of the route.
The flights were welcomed by Deputy First Minister Nicola Sturgeon, who said they were a "good result for Scotland". She added: "They will provide competition on these routes from April 2013, which should lead to a better deal for passengers, as well as offering easier access to Virgin's extensive global network.
"The new flight and cabin crew jobs this will create in Aberdeen are another welcome benefit.
"We are still concerned about the absence of competition on the Glasgow to Heathrow route and will continue to promote its reintroduction; as well as our desire for better direct international connectivity."
The airline said departure times would be co-ordinated to maximise connections with Virgin Atlantic's long-haul network operating out of Heathrow and would use four Airbus 320 aircraft leased from Aer Lingus, which carry about 150 to 180 passengers.
Steve Ridgeway, Virgin Atlantic's chief executive, said the airline planned to fly nearly one million passengers a year on its domestic services.
He said: "Throughout our history, Virgin Atlantic has successfully fought British Airways all over the world and has offered passengers a compelling alternative through our renowned product and service.
"We will look to replicate that in our short-haul flying and challenge the current BA monopoly on these routes, which is causing serious consumer harm."
l Sir Richard Branson could give up control of Virgin Atlantic this week as takeover talks are finalised with Air France-KLM and Delta Air Lines. Delta is said to be poised to buy Singaport Airlines' 49% stake in Virgin, with a view to Air France-KLM buying out much of Sir Richard's holding in due course, leaving him with a small stake.