Heinrich Harrer was born in the Austrian city of Hüttenberg, Carinthia, to a postal worker. From 1933 to 1938 Harrer studied geography and sports at the Karl-Franzens University in Graz. Harrer became a member of the traditional student corporation ATV Graz.

He was designated to participate in the combined Alpine skiing competition at the 1936 Winter Olympics in Garmisch-Partenkirchen. However, the Austrian Alpine skiing team decided to boycott the event due to a conflict regarding the skiing instructor's status as professionals. As a result, Harrer did not participate.

He won the downhill event at the following year's World Student Games.

Harrer was one of the four climbers who made the first ascent of the North Face of the Eiger, Switzerland, with Anderl Heckmair, Fritz Kasparek, and Ludwig Vörg on 24 July 1938. This climb, described by Reinhold Messner as "a glorious moment in the history of mountaineering and a great sensation, since several climbers had previously perished on the Face", made headlines around the world and is recounted in Harrer's book The White Spider of 1958.

Immediately after the Anschluss of March 1938, Harrer on April 1, 1938 joined the SS where he held the rank of Oberscharführer (Sergeant), and on May 1, 1938 he became a member of the Nazi Party. After their ascent of the Eiger's North Face the four climbers were received by and photographed with the Führer which may have been unexceptional and unavoidable. But when in December 1938 Harrer married Lotte Wegener, daughter of the eminent explorer and scholar Alfred Wegener, he did so in SS uniform. In his application for the marriage license that he as an SS Mann had to obtain from the SS-Rasse- und Siedlungshauptamt, Harrer had declared himself a member of the Sturmabteilung (SA stormtroopers) since October 1933, i.e. years before the Anschluss of 1938, when the SA was still illegal in Austria. Harrer later explained this as mere boasting: if already an SA Mann he wouldn't have had to become a member of the Nazi Party when joining the SS.After returning to Europe in 1952 Harrer was cleared of any pre-war crimes and this was later supported by Simon Wiesenthal. In his memoir Beyond Seven Years in Tibet Harrer called his involvement with the Nazi party a mistake made in his youth when he had not yet learned to think for himself.

In 1939 Harrer joined a four-man expedition, led by Peter Aufschnaiter to the Diamir Face of the Nanga Parbat with the aim of finding an easier route to the peak. Having concluded that the face was viable, the four mountaineers were in Karachi at the end of August, waiting for a freighter to take them home. The ship being long overdue Harrer, Chicken and Lobenhoffer tried to reach Persia with their shaky car, but several hundred kilometers northwest of Karachi were put under the "protection" of British soldiers and escorted back to Karachi, where Aufschnaiter had stayed on. Two days later war was declared and on September 3, 1939 all were put behind barbed wire to be transferred to a detention camp at Ahmednagar near Bombay two weeks later. They considered escaping to Portuguese Goa but when further transferred to Dehradun, to be detained there for years with 1,000 other enemy aliens, they found Tibet more promising, the final goal being the Japanese front in Burma or China.

Aufschnaiter and Harrer escaped and were re-captured a number of times before finally succeeding. On April 29, 1944 after lunch, Harrer and six others, including Rolf Magener and Heins von Have (disguised as British officers), Aufschnaiter, the Salzburger Bruno Treipel (aka Treipl) and the Berliners Hans Kopp and Sattler (disguised as native Indian workers), walked out of the camp. Magener and von Have took the train to Calcutta and from there found their way to the Japanese army in Burma. The others headed for the closest border. After Sattler gave up on May 10, the remaining four entered Tibet on May 17, 1944, crossing the Tsang Chok-la Pass (5,896 metres or 19,350 feet) and thereafter split into two groups: Harrer and Kopp, Aufschnaiter and Treipel. On June 17 Treipel, exhausted, bought himself a horse and rode back to the lowlands. Several months later, when the remaining three were still without visas for Tibet, Kopp also gave up and left for Nepal (where he was handed over to the British within few days).

Aufschnaiter and Harrer, helped by the former's knowledge of the Tibetan language, proceeded to the capital of Lhasa which they reached on January 15, 1946, having crossed Western Tibet (passing holy Mount Kailash), the South-West with Gyirong County and the Northern Changthang Plateau.Harrer became a friend of the young 14th Dalai Lama Tenzin Gyatso, who had summoned him to the Potala Palace after having seen him repeatedly in the streets below the palace through his telescope. He taught the Dalai Lama (who was eleven years old when they met) much about the outside world and effectively served as his tutor, in subjects ranging from geography to English. The Dalai Lama has often credited Harrer's later writings about Tibet as having helped focus international attention on the Tibetan people after the Communist Chinese gained administrative control.

After the Communist army took control in Tibet in 1950, Harrer returned to Austria where he documented his experiences in the books Seven Years in Tibet and Lost Lhasa. Seven Years in Tibet was translated into 53 languages, was a bestseller in the United States in 1954, sold three million copies and was the basis of films by the same title in 1956 and 1997. He was portrayed by Brad Pitt in the latter film.

He also took part in a number of ethnographic as well as mountaineering expeditions: Alaska, the Andes, Ruwenzori (Mountains of the Moon) in Africa. He explored the Amazon with the former king Leopold III of Belgium. Harrer made the first ascents of Mount Deborah and Mount Hunter (both in Alaska) in 1954. In 1962 he was the leader of the team of four climbers who made the first ascent of the Carstensz Pyramid (Puncak Jaya) in western New Guinea, the highest peak in Oceania. This and his pioneering expedition to reach the Neolithic stone axe quarries at Ya-Li-Me are recorded in his memoir I Come From The Stone Age.

Harrer wrote more than 20 books about his adventures, some including photographs considered to be among the best records of traditional Tibetan culture. In the early 1980s, he visited Tibet again, and wrote a sequel to Seven Years in Tibet titled, Return to Tibet. He made approximately 40 documentary films and founded a museum about Tibet in Austria. In October 2002, the Dalai Lama presented Harrer with the International Campaign for Tibet's Light of Truth Award for his efforts to bring the situation in Tibet to international attention. Harrer died on 7 January 2006 in Friesach, Austria at the age of 93.