Bed Bahadur Sunuwar was one of more than 150 local and foreign runners in the race, which began at Nepal's base camp.
The annual run marks the anniversary of the first summit of the peak by Tenzing Norgay and Edmund Hillary in 1953.
The winner completed the race, which ended about 2,000 metres further down the slopes, in four hours and 10 seconds.
"The route is very challenging but amazing too. I feel proud to be the winner," the 29-year-old man said.
Around 30 local runners were joined by about 130 from around the world, including the UK, US, China and Australia. A Nepali man was also the winner in 2015.
This is the first climbing season on Everest after two seasons hit by disasters - an avalanche that killed 16 mountain guides in 2014, and a fatal earthquake in 2015.
The 2016 season has not been without tragedy though, with several deaths from altitude sickness during a particularly busy period on the peak. On Friday, officials announced they had found the body of an Indian climber on the upper slopes, taking the season's death toll to four.
A Nepali soldier has won the world's highest marathon on Mount Everest.