Gold investor Thomas Kaplan also donated the proceeds from a Christie's auction on Thursday of a second Mark I Spitfire he owned to the Royal Air Force Benevolent Fund and Panthera, a wildlife charity.
The two planes -- the earliest models of Spitfire -- both crashed on French beaches during the battle of Dunkirk in 1940 and sank into the sand.
They were recovered and are now the only two of those models in existence that can still fly, following a painstaking restoration lasting years.
The Spitfire donated to the museum took to the skies for a display on Thursday. The other one was later auctioned for USD 4.8 million.
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The auction house said in a statement that the plane's flying officer Peter Cazenove, who survived but was taken prisoner, had radioed back to base shortly before being forced to make a beach belly-landing: "Tell mother I'll be home for tea!"
Kaplan said that the donations were "to pay homage to those who Churchill called 'the Few', the pilots who were all that stood between Hitler's darkness and what was left of civilisation".
The plane was being shown off at the air force museum in Duxford north of London, which hosted Britain's first squadron to fly Spitfires and where the Spitfire originally flew from in 1940.