Using measurements from an infrared telescope in Hawaii, a UK and US team found evidence for temperatures as high as 1,500C - hundreds of degrees warmer than anywhere else on the planet.
The spot is three Earth diameters across.
The freshly discovered spike in temperature, detected using a spectrometer at the Nasa Infrared Telescope Facility (IRTF) in Mauna Kea, Hawaii, offers a solution.
Several hundred km directly above the clouds of the Great Red Spot, the hotspot suggests that high-altitude heat is somehow created by the turmoil beneath.
"Several people have argued that it's likely that the heat comes from below, but the observations have never backed them up," Dr Stallard said.
He and his colleagues don't know exactly what is causing the heat, but they have some ideas. It could be driven by devastating Jovian thunderclaps, rumbling upwards from the churning red clouds of the Solar System's biggest storm.
"You get some kind of acoustic event, probably thunder or something like that - or possibly other forms of sound energy - and that propagates directly upwards," Dr Stallard explained.
"That wave will continue going upwards until it reaches a lower-density region at the top of the atmosphere, and then it breaks and deposits all that wave energy into the top of the atmosphere, just like waves break on the shore - as the water gets thinner, it's less able to carry that wave and so it breaks and you see lots of energy."
There is a precedent for such sound-driven warming much closer to home, according to Dr O'Donoghue.
"There is some evidence in Earth's atmosphere, above storms and above features such as mountains - the Andes mountains in fact - that there are acoustic waves emanating from them, and that they propagate up into the atmosphere and cause heating there," he said.
So, gigantic thunderstorms generate such huge thunderclaps that they can actually heat the atmosphere to 1500 degrees celsius. Wild.
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