Pulling away in plume of white steam, the 97-tonne green engine pulled out at 0740 GMT with some 300 passengers on board to applause from a crowd of enthusiasts who had come to witness its rebirth.
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The Flying Scotsman is set to arrive at 1230 GMT in York, a historic city some 280 kilometres (175 miles) north of London, before heading to the city's National Railway Museum where it will stay until the beginning of March.
The train will then spend the coming months on tourist trips and featuring in exhibitions.
Restoring the famous engine cost around £4.2 million (5.3 million euros, $5.8 million).
Thursday sees the locomotive's first official outing since it returned to the rails last January in Bury, northwest England, for a series of tests.
"It's a historic day," said Paul Kirkman, director of the National Railway Museum.
"This celebratory journey marks a new stage in this steam icon's long and colourful history, and is a tribute to all the people who have worked so hard to make this happen, from those that have worked on the restoration itself to the public that donated to our appeal to bring this legend back to life."
"It's great to see this magnificent symbol of Britain's railway heritage and technology once again running on our tracks," added Peter Hendy, chairman of Network Rail, which runs Britain's rail network.
The National Railway Museum bought the Flying Scotsman in 2004, partly thanks to funds donated by the public. Restoration work started in 2006.
Built in 1923, the locomotive was the first steam engine officially to hit 160 km/h (100 mph) and the first to link London to Edinburgh in a single journey.
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After being retired in 1963, the Flying Scotsman crossed the Atlantic to pull tourist trains on the West Coast of the United States.
Bought in 1973 by a British billionaire, William McAlpine, the locomotive returned to Britain and passed through the hands of several owners.
Fully renovated in the late 1990s, the locomotive pulled the Venice Simplon-Orient Express on tourist trips from Victoria station in London.
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