It hosts scheduled passenger service from Ottawa, Montreal, Rankin Inlet, and Kuujjuaq on carriers such as Canadian North, and from smaller communities throughout eastern Nunavut.

In mid-October, trawlers Lark, Polarbjoern, and Selis reached the vicinity, but owing to inaccurate charts (dating from the 1865 expedition of Charles Francis Hall) could not find the Roosevelt site.

[10] When the station relief and base construction expedition arrived next July, both the Crowell and Roosevelt sites were rejected in favour of a level meadow discovered along the Sylvia Grinnell River on mainland Baffin Island.

[13] The initial mission of the Crystal sites was to provide long-range weather information to the combat forces then building up in the United Kingdom.

The original plan, briefed by Captain Roosevelt to USAAF Chief Henry "Hap" Arnold and others at the Atlantic Conference in August 1941, called for Frobisher Bay to be a node in a northern alternate air route, running from Churchill, Manitoba, via Southampton Island over Frobisher to Bluie West Eight and Bluie East Two in Greenland, rejoining the main route in Iceland.

[15] The later success of the main air route via Bluie West One and the spring 1943 victory in the Battle of the Atlantic led to cancellation of the Crimson project in late 1943, and the associated airfields were reduced to weather, communications, and logistics duties.

Crews departing westward from Prestwick or Shannon in those years preferred to route via Iceland (or the Azores) to Gander, thence to New York City or elsewhere.

The place remained prominent as a regional airport, continued in its strategic role of sustaining the Distant Early Warning Line (DEW), supported the occasional military exercise or scientific expedition, and was a key stopover on the North Atlantic ferry route.

By the 1970s, the company's fleet of de Havilland Canada DHC-6 Twin Otters and Douglas DC-3s was serving many small Arctic communities from YFB, carrying passengers, mail, groceries, and other essentials.

The main terminal was constructed c.1986 and had become outdated as a result of increased traffic, limited post-security waiting area[20] and subsiding taxiway,[21] the Nunavut government planned an overhaul of the airport that was expected to cost $250–300 million.

[20] Over the years several international flights have been diverted to Iqaluit due to technical reasons,[27] air rage[28] or on-board medical emergencies with no deaths being reported.

[29] On 31 May 1996, Virgin Atlantic flight 7 from London to Los Angeles made an emergency landing at Iqaluit after a passenger had a heart attack.

[30] The Airbus A380, the world's largest passenger jet, conducted cold weather testing from Iqaluit Airport during February 2006 – its first North American visit.

Airport staff cited low landing fee, sufficient runway length, and minimal air traffic movement all helped in the decision making.

[33] Following from these previous successful visits by prototype Airbus aircraft, the company sent the first A320neo with CFM International LEAP engines to be tested in January 2016.

As part of the type's first visit to North America, the jet performed several circuits in the subzero temperatures before departing back to Toulouse–Blagnac Airport.

[34] In December 2005 the Government of Nunavut announced that it would spend $40 million to repair the runway, build a new emergency services facility and a new terminal.

[41] Air Greenland, with Canadian North providing connections to Ottawa, Montreal and Kuujjuaq, will relaunch a route between Nuuk and Iqaluit during the 2024 summer.