It was discovered at the bottom of a wardrobe wrapped in a blanket after a science-fiction memorabilia collector died, Trevanion & Dean Auctioneers said.
The puppet was sold earlier at an auction in Whitchurch, Shropshire.
At its peak, the science-fiction series was attracting an audience of 100 million fans in 66 countries.
Thunderbirds, which was first aired on TV screens in 1965, told the story of the Tracy family who form a secret organisation dedicated to saving human life.
Auctioneer Christina Trevanion said the seller, the brother of the previous owner, had "looked and looked and looked" for the puppet after his brother's death, before finally finding it.
Asked why the puppet was hidden in a wardrobe, the auctioneer said: "I think [the man] was very precious about her.
"These things, if left out... would gather dust. Her wig is real hair. It would need constant cleaning.
"She was the absolute star of [the man's] collection."
She said plenty of replicas were made, but puppeteers on the 1960s TV series and leading UK puppet-makers had confirmed it as an original.
Ms Trevanion added that the "utterly unique" puppet from "an iconic series"  had generated interest from the US, Japan and New Zealand ahead of the auction.
The auctioneer said: "People watched who were children in the 1960s. There was a generation which saw repeats in the 80s and 90s.
"Every single generation has very fond memories of Thunderbirds."
A Lady Penelope puppet used in the hit TV show Thunderbirds has sold for £19,000 at auction.