The World War II fighter plane was flying near the RAF Coningsby base in Lincolnshire when it came down in a field shortly after 1:00 pm (1200 GMT).
Police and emergency services rushed to the scene, where the male pilot, who has not yet been named, was declared dead.
"It is with great sadness that we must confirm the death of an RAF pilot in a tragic accident near RAF Coningsby today," said a spokesperson for the Ministry of Defence.
"The pilot's family have been informed and we ask that their privacy is respected at this difficult time."
Local police said it was a single occupant aircraft and nobody else was involved.
An investigation is due to take place.
Prime Minister Rishi Sunak said in a post on the social media site X that his "thoughts" were with the victim's family and loved ones after the "tragic event".
Opposition leader Keir Starmer said he was "deeply saddened" by the news.
RAF Coningsby is home to the Battle of Britain Memorial Flight, a collection of wartime fighter and bomber aircraft that take part in air shows and memorial displays.
Only a few dozen airworthy Spitfires remain, including six based at RAF Coningsby.
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