Lacing up his shoes and hitting the road helps him relieve stress, gives him quiet time to think and keeps him fit.
But when he recently started experiencing knee pain, the 38-year-old Edmonton filmmaker/anthropologist feared he may have reached the end of the road as a runner.
"It was actually quite scary," Thompson recalled.
It's a fear many recreational runners who struggle with pain and injury have faced.
That fear inspired Thompson to make "The Perfect Runner," a documentary airing Thursday on CBC's "The Nature of Things" that examines the evolution and science of running.
"I realized that some of the science out there is telling us that a lot of the running techniques you see are inefficient and damaging our bodies," Thompson said in an interview. "So going into this film was part of a process of learning how to run properly as a runner and changing how I run so that it's more sustainable."
It was a journey that took Thompson and his crew to some of the most remote corners of the world, from the Canadian Rockies to Arctic Siberia and the Ethiopian highlands.
The film — which features breathtaking cinematography — explores how our ancestors used their unique ability as endurance runners to evolve from "a tree climbing ape to dominate our world."
To help understand the science and history, the filmmakers make a stop in Africa's desolate Great Rift Valley, the birthplace of humankind.
"It is the most persistently inhabited place on the planet," Thompson says in the film. "For at least 10 million years, our ancestors have lived and evolved in this place."
The Gemini Award-winner also interviews several scientists and experts, including Harvard professor Daniel Lieberman and Canadian sports chiropractor Larry Bell.
A handful of Canadian athletes, including sprinter Emanuel Parris and retired 400-metre runner Tyler Christopher, also have cameos, some beautifully depicted running in slow motion using state-of-the-art technology.
Early humans, the film explains, didn't have speed on their side but were able to survive thanks to their unmatched endurance that allowed them to outrun their prey.
The documentary says our ancestors became "persistence hunters" who could run down other animals to the point of exhaustion.
"Humans are built to run," said Thompson. "On a hot day, we can outrun all the animals in our environment."
Thompson also takes his cameras to Chukotka in northeastern Russia, where he spends time with a remote community of nomadic reindeer herders. For them, running with their animals is necessary for survival.
"We live in a world of the mind, not the body," Thompson said. "So we had to go to the edges of our world to find places where it's not so easy to survive."
Thompson says what he discovered in Russia was amazing.
"These people run all day long," he said. "They're cowboys without horses."
From the Siberian tundra, the film moves to the Ethiopian highlands where Thompson examines how one of the world's poorest countries has also produced some of its top runners.
One of the secrets, Thompson discovers, is that most Ethiopian athletes start out running in bare feet.
Barefoot running has become trendy in the recreational running community recently, thanks in part to Christopher McDougall's bestselling book "Born to Run."
Thompson explores the controversial issue in the film, visiting Lieberman's lab at Harvard. The professor of human evolutionary biology has done extensive research on barefoot running.
What Lieberman has found is that people who wear traditional running shoes with thick, supportive soles tend to land on their heel with each stride, which can be damaging to the body.
When runners land on their heel, Thompson explains, the body is not using the natural "springs'' in the feet.
Lieberman has found that runners who run in bare feet tend to land on the ball of their foot, which is the way humans were designed to run.
"His research shows that fewer of those people experience injuries," said Thompson.
In the film, Lieberman analyzes Thompson's running style on a special treadmill that measures impact.
The difference between the impact his body experienced in a traditional running shoe versus barefoot running was so dramatic that he has changed the way he runs, focusing on striking with his forefoot rather than his heel. He also includes short barefoot runs in his training regimen to strengthen his feet and ankles.
"There was a period of transition where I had all sorts of soreness in my feet and my calves," said Thompson, who does not believe people should run more than a few kilometres in bare feet. "But very quickly that disappeared and I got used to landing on my forefoot."
The knee pain that he had been struggling with eventually disappeared too.
"I was healed," he said. "I run without pain now and the crisis I was having as a runner before I started the project seems to have disappeared."
To fully test the theory that humans are the world's best endurance runners, Thompson attempts to compete the Canadian Death Race, a gruelling 125-kilometre run through the Rockies.
"I have to admit, I thought 'This is going to make good TV but I'll never get through half of this race,'" he recalled.
But Thompson wanted to try. When the day finally came, he surprised himself.
"It was an extraordinary experience," he said. "I really enjoyed it. I didn't get to the end of the race. I ran 103 kilometres. But I did manage to climb all three peaks in the race. It was such a special thing to realize that I could do that a year after thinking it was completely impossible."
It's a lesson he hopes his audience will come away with.
"You're capable of a lot more than you think you are if you train, if you spend less time at a desk and more time out there using your body for what it's meant to do, it's extraordinary what you can accomplish," he said.
And he's not done with the Death Race. Thompson plans to do it again this summer and this time, he wants to finish.
"The Perfect Runner" airs Thursday on CBC (check local listings).