After studying anthropology, Stefansson went on his first Arctic expedition in 1906-1097; this trip was led by the Danish explorer Ejnar Mikkelson. They traveled to Herschel Island (in the Beaufort Sea just north of the Yukon), and Stefansson began studying the language and culture of the Inuit and the Mackenzie River Indians. Stefansson met Roald Amundsen towards the end of this trip.

In 1908, Stefansson returned to the Arctic with the Canadian zoologist Rudolph M. Anderson, traveling to Herschel Island, Cape Parry, and the south side of Victoria Island. They encountered the Copper Inuit (a previously unknown group of Inuits who made and used copper tools). Stefansson stayed with the Copper Inuit until 1912. Since many of these Native Americans had European features and some had blue eyes, Stefansson theorized that they were a mixture of Native Americans and early Norse explorers or the lost expedition of Sir John Franklin. Although his theory was not accepted, it did give Stefansson quite a bit of notoriety.

Stefansson's last Arctic trip was in 1913, when he was appointed head of a Canadian scientific expedition. The expedition sailed from Seattle, Washington, USA, in an old sealing ship Karluk (Bob Bartlett was Captain), but were stuck in the ice north of Alaska in August, 1913. In September, Stefansson and a small group left the ship to hunt for food, but never returned to the ship, since it drifted away (as the ice moved west). The ship was eventually crushed by the ice but most of the crew survived. Stefansson and his small group drifted on ice floes and explored Northern Canada, returning in 1918.

He organized another Arctic expedition in 1921-1924 (which he did not go on). Stefansson Island, at the tip of Victoria Island, was named for him in 1952. Stefansson spent the latter part of his life as Director of Polar Studies at Dartmouth College (Hanover, New Hampshire, USA). He wrote many books, including My Life with the Eskimos (1913), The Friendly Arctic (1921), and Discovery (Stefansson's autobiography, published in 1964, after his death).