The modest, 1930s-era oak chair was part of a mismatched set of four that Rowling was given for free when she was a single mother living in subsidized housing in the Scottish city of Edinburgh.
Heritage Auctions said it sold for $394,000, including taxes -- nearly 14 times the price that it last fetched at auction in 2009.
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The 50-year-old author used the chair to write "Harry Potter and the Philosopher's Stone" and "Harry Potter and the Chamber of Secrets" published in 1997 and 1998, respectively.
"This was the comfiest one, which is why it ended up stationed permanently in front of my typewriter, supporting me while I typed," Rowling wrote in a letter accompanying the chair, said the auction house.
"My nostalgic side is quite sad to see it go, but my back isn't," she added.
Rowling donated the chair in 2002 to an auction benefitting the National Society for the Prevention of Cruelty to Children after adorning it with words in pink, gold and green paint.
"You may not find me pretty but don't judge on what you see," she wrote, along with "I wrote Harry Potter while sitting on this chair" and her signature, the auction house said.
It sold again at auction in 2009 for $29,117, Heritage said.
"A small piece of history connected to the mythology of the Wizarding World and one of the most beloved characters in children's literature," said the auction house.
The seven-part "Harry Potter" series became a global phenomenon, translated into 67 languages. It sold more than 450 million copies and was credited with reviving children's interest in reading.
Also adapted into box office blockbuster films, "Harry Potter" made Rowling the first female novelist billionaire.
In 2012, Forbes dropped her from its billionaire list, attributing it to Rowling's charitable donations and high tax rates in Britain.
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