Karnazes grew up in Los Angeles, where he began running home from kindergarten; he took up running so that he wouldn’t have to burden his mother with rides home from school every day.

At first, Karnazes ran direct routes from school to his home. Later, he began to run diversionary routes that would extend his run and take him into uncharted territory. By third grade he was participating in and organizing short running events with other kids. As Karnazes grew older, he began testing his limits: by age eleven he had hiked rim-to-rim across the Grand Canyon and had climbed Mount Whitney, the highest mountain in the contiguous United States; for his 12th birthday, he cycled the 40 miles to his grandparents' home for fun, without first telling his parents.

In junior high, Karnazes met Bernard Emil Weik II, a track coach who became Karnazes’ mentor and introduced him to the appeal of long-distance running. Weik's basic running instructions were simple: "Go out hard and finish harder." Using this motto as a basis, that season Karnazes won the one-mile California State Long-Distance Championship held on the Mt SAC track. At the end of the race, coach Weik commented: "Good work son, how'd it feel?" To this Karnazes replied: "Well, going out hard was the right thing to do. It felt pretty good." The coach replied: "If it felt good, you didn’t push hard enough. It’s supposed to hurt like hell." A week after the race, Karnazes' father's job was transferred to San Clemente. These were the last comments the coach ever said to Karnazes, who has stated that he lives by these words to this day.

In 1976, as a high school freshman, Karnazes joined the cross country team under Benner Cummings. Cummings’ running theory was that running is about finding your inner peace; his motto was "run with your heart." That season, Karnazes was awarded "Most Inspirational" team member. Karnazes also ran his first endurance event that year, a fundraising run on a track for underprivileged children, finishing in just under six hours and raising a dollar a lap from his sponsors. While most students ran only 10-15 laps around the track, he ran 105.

Karnazes was not compatible with his high school track coach and stopped running for fifteen years. He resumed running on his 30th birthday with an impromptu all-night, 30-mile trek in his underwear and old lawn-mowing shoes.

In 2004, Karnazes was named one of GQ's "Best Bodies of the Year".

Karnazes has completed a number of endurance events, mostly running events, but also a swimming event. Most notably, he ran 135 miles nonstop across Death Valley in 120°F (49°C) temperatures, and a marathon to the South Pole at ?40°F(-40°C). In 2006, he ran 50 marathons, in all 50 US states, in 50 consecutive days, finishing with the New York City Marathon, which he completed in three hours and thirty seconds.

Other highlights are:

• Overall Winner, 4 Deserts Race Series, 2008

• Competitor magazine Endurance Athlete of the Year Award winner, 2008, 2006, 2005

• ESPN ESPY Award winner, “Best Outdoor Athlete,” 2007

• Winner, Vermont Trail 100 Mile Endurance Run, 2006

• Two-time Emmy Award winner, 2005, 2007

• American Ultrarunning Team, World Championships, 2005, 2008

• Men’s Journal, Adventure Hall of Fame, 2005

• Winner, Badwater Ultramarathon, 2004
• in 80 hours and 44 minutes without stopping (2005)

• in 24 hours on a treadmill, 2004

• single-handedly completed the Providian Saturn Relay six times

• Eleven-time 100-Mile/1 Day Silver Buckleholder at the Western States Endurance Run (i.e., better than ten twenty-four hour finishes), 1995-2006

• Outside magazine, Ultimate Top 10 Outdoor Athletes, 2004

• Swimming across the San Francisco Bay

50 marathons in 50 states on 50 consecutive days

The 50/50/50 was fifty marathons in fifty states in fifty consecutive days, beginning with the Lewis and Clark Marathon in St. Louis on September 17, 2006, and finishing with the New York City Marathon on November 5. Eight of the fifty races were conventional marathons. Since marathon races are typically held only on Saturdays and Sundays, on the other days Karnazes (accompanied by between 1 and 50 runners) ran the course of a marathon in each state using the help of the Race Director and staff of each event to officially run the certified course, but on a different day than the “live” event. (For example, as part of the 50/50/50, Karnazes ran the official course of the Boston Marathon, but not the race itself, which is held in mid-April.)

Karnazes overcame the endurance and logistical difficulties of this goal, and Karnazes finished the final marathon, the NYC Marathon on the official race day, in 3 hours and 30 seconds. He weighed 154 lbs at the start, and 153 lbs at the end.

After finishing the 50/50/50, Karnazes decided to run home to San Francisco from New York City. He was expected to finish the trip in January 2007. However Karnazes chose to end this trek on December 15, 2006, in St. Charles, Missouri, to spend more time with his family.

The adventure was the primary subject of film director JB Benna's 2008 film entitled UltraMarathon Man: 50 Marathons - 50 States - 50 Days, which was the first feature film about Karnazes. The film was produced by Journeyfilm, had a national theatrical release in 300 screens in 2008 and was released on DVD and Blu Ray in 2009.

A similar project, undertaken by Sam Thompson to raise money for victims of Hurricane Katrina, was finishing as Karnazes began his project. Thompson ran 51 marathons (all 50 states and D.C.) in 50 days.

Dean is a businessman with a notable professional career working for several Fortune 500 companies and startups. He graduated from the McLaren School of Business & Management. He is also a motivational speaker.

In 1995, Karnazes founded Energy Well Natural Foods in San Francisco and he remains president of the company, now called Good Health Natural Foods. He holds graduate degrees in Science and Business. Karnazes resides in San Francisco, California, with his wife, Julie, and two children, Alexandria and Nicholas. Karnazes is also a regular columnist for Men's Health.

Dean was featured in the August 19, 2010 episode "Hammer Head" of Stan Lee's Superhumans documentary television series where it was shown that Dean is able to somehow keep his lactic acid level from building up, actually reducing and maintaining the reduction over long periods of time.