Police said the man and a companion had climbed Mount Sonder, which is the fourth-highest peak in the Northern Territory, and were on the descent when they separated.
Duty Superintendent Rob Burgoyne told ABC Darwin: "It's about 1,300 metres tall and the actual walk that they undertook was about 16 kilometres there and back — so quite a hike."
The 40-year-old man he was walking with told police the 33-year-old ran off on their way back and appeared to have taken a wrong turn.
"They both descended the mountain, unfortunately it appears the deceased took a wrong turn at that stage," Duty Superintendent Burgoyne said."His partner made it back to the Redbank Gorge carpark and raised the alarm, but unfortunately the 33-year-old didn't arrive and his body was eventually located about 400 metres down the track where he'd turned the wrong way.
"It was about three hours from when he was last seen and when his body was found."
Police said investigations were ongoing but it was not believed there were any suspicious circumstances surrounding the death.
Temperatures reached 42C
The Bureau of Meteorology confirmed Alice Springs reached a top of 42 degrees Celsius on Wednesday, which Duty Superintendent Burgoyne said would have made trekking conditions difficult.
"We do know he had water with him, but he did do a very foolish thing in that he apparently ran away from his companion after the descent," he said."It wouldn't be a terribly advisable thing to do in 40-degree heat, to actually sprint away."
Authorities warn against embarking on the long trek in the heat because it comes with a high risk of becoming dangerously dehydrated, Chris Day from Parks and Wildlife said.
"It's almost physically impossible to put back the fluids that you're going to lose as quickly as you're losing them, and unfortunately people become dehydrated very rapidly before even realising that it's even happening," Mr Day said.
"Unfortunately it is too late, quite often, once people realise they're in trouble."
Mount Sonder, the final section of the 223-kilometre Larapinta Trail which the men were on, is a steep, rocky incline with an exposed landscape.
"Its a very exposed mountain walk," Mr Day said.
"There's no big shady trees and it's very rocky, so when you've got a hot day like we had (on Tuesday) we've got a lot of radiated heat coming back off the rocks.
"Obviously on days when temperatures are forecast to be in the 40s, we strongly advise against doing any longer walks."