The first human inhabitants of Ellesmere Island were small bands drawn to the area for Peary caribou, muskox, and marine mammal hunting about 2000–1000 BCE.
As was the case for the Dorset (or Palaeoeskimo) hunters and the pioneering Neoeskimos, the Post-Ruin Island and Late Thule culture Inuit used the Bache Peninsula region extensively both summer and winter until environmental, ecological, and possibly social circumstances caused the area to be abandoned. It was the last region in the Canadian High Arctic to be depopulated during the Little Ice Age, attesting to its general economic importance as part of the Smith Sound culture sphere of which it was occasionally a part and sometimes the principal settlement component.
Vikings from the Greenland colonies reached Ellesmere Island, Skraeling Island, and Ruin Island during hunting expeditions and trading with the Inuit groups. Unusual structures on Bache peninsula may be the remains of a late-period Dorset stone longhouse.
The first European to sight the island after the height of the Little Ice Age was William Baffin in 1616. Ellesmere Island was named in 1852 by Edward Inglefield's expedition after Francis Egerton, 1st Earl of Ellesmere. The US expedition led by Adolphus Greely in 1881 crossed the island from east to west, establishing Fort Conger in the northern part of the island. The Greely expedition found fossil forests on Ellesmere Island in the late 1880s. Stenkul Fiord was first explored in 1902 by Per Schei, a member of Otto Sverdrup's 2nd Norwegian Polar Expedition.
The Ellesmere Ice Shelf was documented by the British Arctic Expedition of 1875–76, in which Lieutenant Pelham Aldrich's party went from Cape Sheridan (82°28′N 61°30′W / 82.467°N 61.500°W / 82.467; -61.500 (Cape Sheridan (Ellesmere Island))) west to Cape Alert (82°16′N 85°33′W / 82.267°N 85.550°W / 82.267; -85.550 (Cape Alert (Ellesmere Island))), including the Ward Hunt Ice Shelf. In 1906 Robert Peary led an expedition in northern Ellesmere Island, from Cape Sheridan along the coast to the western side of Nansen Sound (93°W). During Peary's expedition, the Ice Shelf was continuous; a modern estimate is that it covered 8,900 km2 (3,400 sq mi).
In 2011, Jon Turk and Erik Boomer completed the first known circumnavigation of Ellesmere Island.
Ellesmere Island is separated to the east by Nares Strait from Greenland, to the west by Eureka Sound and Nansen Sound from Axel Heiberg Island, and to the south by Jones Sound and Cardigan Strait from Devon Island.
Ellesmere Island contains Canada's northernmost point, Cape Columbia at 83°6′41″N.
More than one-fifth of the island is protected as Quttinirpaaq National Park (formerly Ellesmere Island National Park Reserve), which includes seven fjords and a variety of glaciers, as well as Lake Hazen, North America's largest lake north of the Arctic Circle. Barbeau Peak, the highest mountain in Nunavut (2,616 m or 8,583 ft) is located in the British Empire Range on Ellesmere Island. The most northern mountain range in the world, the Challenger Mountains, is located in the northeast region of the island. The northern lobe of the island is called Grant Land.
In July 2007, a study noted the disappearance of habitat for waterfowl, invertebrates, and algae on Ellesmere Island. According to John P. Smol of Queen's University in Kingston, Ontario, and Marianne S. V. Douglas of the University of Alberta in Edmonton, warming conditions and evaporation have caused low water levels and changes in the chemistry of ponds and wetlands in the area. The researchers noted that "In the 1980s they often needed to wear hip waders to make their way to the ponds...while by 2006 the same areas were dry enough to burn."
Large portions of Ellesmere Island are covered with glaciers and ice, with Manson Icefield (6,200 km2 or 2,400 sq mi) and Sydkap (3,700 km2 or 1,400 sq mi) in the south; Prince of Wales Icefield (20,700 km2 or 8,000 sq mi) and Agassiz Ice Cap (21,500 km2 or 8,300 sq mi) along the central-east side of the island, and the Northern Ellesmere icefields (24,400 km2 or 9,400 sq mi).
The northwest coast of Ellesmere Island was covered by a massive, 500 km (310 mi) long ice shelf until the 20th century. The Ellesmere Ice Shelf shrank by 90 percent in the twentieth century due to warming trends in the Arctic, particularly in the 1930s and 1940s, a period when the largest ice islands (the 200 square mile T1 and the 300 square mile T2 ice islands) were formed leaving the separate Alfred Ernest, Ayles, Milne, Ward Hunt, and Markham Ice Shelves. A 1986 survey of Canadian ice shelves found that 48 km2 (19 sq mi) or 3.3 km3 (0.79 cu mi) of ice calved from the Milne and Ayles ice shelves between 1959 and 1974. The Ward Hunt Ice Shelf, the largest remaining section of thick (>10 m, >30 ft) landfast sea ice along the northern coastline of Ellesmere Island, lost 600 km (370 mi) of ice in a massive calving in 1961–1962. It further decreased by 27% in thickness (13 m or 43 ft) between 1967 and 1999.
The breakup of the Ellesmere Ice Shelves has continued in the 21st century: the Ward Ice Shelf experienced a major breakup during summer 2002; the Ayles Ice Shelf calved entirely on August 13, 2005; the largest breakoff of the ice shelf in 25 years, it may pose a threat to the oil industry in the Beaufort Sea. The piece is 66 km2 (25 sq mi). In April 2008, it was discovered that the Ward Hunt shelf was fractured, with dozens of deep, multi-faceted cracks and in September 2008 the Markham shelf (50 km2 or 19 sq mi) completely broke off to become floating sea-ice.
Schei and later Nathorst described the Paleocene-Eocene (ca. 55 Ma) fossil forest in the Stenkul Fiord sediments. The Stenkul Fiord site represents a series of deltaic swamp and floodplain forests. The trees stood for at least 400 years. Individual stumps and stems of >1 m (>3 ft) diameter were abundant, and are identified as Metasequoia and possibly Glyptostrobus. Well preserved Pliocene peats containing abundant vertebrate and plant macrofossils characteristic of a boreal forest have been reported from Strathcona Fiord.
In 2006, University of Chicago paleontologist Neil Shubin and Academy of Natural Sciences paleontologist Ted Daeschler reported the discovery of the fossil of a Paleozoic (ca. 375 Ma) fish, named Tiktaalik roseae, in the former stream beds of Ellesmere Island. The fossil exhibits many characteristics of fish, but also indicates a transitional creature that may be a predecessor of amphibians, reptiles, birds, and mammals, including humans.
In 2011, Jason P. Downs and co-authors described the sarcopterygian Laccognathus embryi from specimens collected from the same locality that Tiktaalik was found.
Ellesmere Island is noted as being the northernmost occurrence of eusocial insects; specifically, the bumblebee Bombus polaris. There is a second species of bumblebee occurring there, Bombus hyperboreus, which is a parasite in the nests of B. polaris.
While non-eusocial, the arctic woolly bear moth (G. groenlandica) can also be found at Ellesmere Island. While this species generally has a 10-year life cycle, its life is known to extend to up to 14 years at both the Alexandra Fiord lowland and Ellesmere Island.
In 2016, the population of Ellesmere Island was recorded as 191. There are three settlements on Ellesmere Island, Alert (pop. 62), Eureka (permanent pop. 0, but home to a small temporary population), and Grise Fiord (pop. 129), Politically, it is part of the Qikiqtaaluk Region.
Canadian Forces Station (CFS) Alert is the northernmost settlement in the world. With the end of the Cold War and the advent of new technologies allowing for remote interpretation of data, the overwintering population has been reduced to 62 civilians and military personnel as of 2016.
Eureka, which is the third northernmost settlement in the world, consists of three areas, "Eureka Aerodrome" which includes "Fort Eureka" (the quarters for military personnel maintaining the island's communications equipment), the Environment Canada Weather Station, and the Polar Environment Atmospheric Research Laboratory (PEARL), formerly the Arctic Stratospheric Ozone (AStrO) Observatory. Eureka has the lowest average annual temperature and least precipitation of any weather station in Canada.
In the 2013 American superhero film Man of Steel, Ellesmere Island was the site of a combined US-Canadian scientific expedition to recover an ancient Kryptonian spaceship buried in the glacial ice pack.
The island was the location for the 2014 BBC programme Snow Wolf Family and Me.
It is the location of the NSA Camp Northern Light listening post in Z Nation.