On August 25, 1811, after a perilous trip along the coasts of Labrador and Ungava Bay, Benjamin Gottlieb Kohlmeister and George Kmoch arrived at an Inuit camp on the east shore of the Koksoak.

According to their journal, they found the Inuit of the Koksoak River very interested in having a Moravian mission in the area, but after reaching a little farther than "Pilgerruh" ("Pilgrim's Rest") on "Unity's Bay" they turned back for home.

[9] Attracted by the missionaries' praise of the location,[10] the Hudson's Bay Company established a permanent station on the east shore of the Koksoak River in 1830,[6] at a site about 5 km (3.1 mi) downstream from the present settlement.

[6] By 1833, Fort Chimo comprised seven buildings in a defensive square, principally trading in caribou hides and white fox and marten pelts.

[6] Erlandson ultimately discovered bountiful trapping far to the south in the highlands around Lake Petitsikapau; he briefly succeeded Finlayson as acting factor but was replaced when a brig delivered John McLean to his new post in 1837.

The fort did not reopen until 1866, when it was thought necessary to curtail the trade going to the Moravians in the area and the steamboat Labrador made resupplying the distant outpost easier.

[6] A sloop, a steamer, and outposts at the mouths of the Whale and George Rivers helped carry out the salmon catch each August, which was salted on site for use, sale, and export.

[6] Amid the Second World War, the United States Army Air Forces (USAAF) surveyed the area from amphibious aircraft out of Gander on July 12, 1941 and established the Crystal 1 weather station on the western shore of the Koksoak on October 10, 1941.

The high cost of maintaining and supplying the base, however, led to it being shuttered in late summer 1952 and its equipment and personnel moved to Frobisher Bay (now Iqaluit) on Baffin Island.

With more Inuit settling in the area during this time to assist the base, a Catholic mission was established in 1948 and was followed by an infirmary, a school, and a weather station.

[citation needed] The HBC outpost at Fort Chimo was closed for months of repairs in 1957 after a major fire, and the post was moved closer to the airfield in 1960.

Although less snowfall is received compared to the more coastal Nain further south, the influence of the current contributes to a sizeable snow tally for a climate that cold.

In spite of this, Kuujjuaq being situated with a direct landmass link to its south for thousands of kilometres can contribute to warm southerlies reaching the settlement, bringing temperatures above 30 °C (86 °F).

Unlike Inukjuak directly on the Hudson Bay shore, Kuujjuaq thus has a greater continental warmth impact on its summers, and consequently lies below the tree line.