Northern Fur Seals have one of the longest and most complex histories of commercial harvesting, which began when the main breeding colonies were discovered in the late 18th century; exploitation continued through until 1984. Numerous international treaties and agreements were put in force over time in efforts to manage this species. There were many periods of decline and recovery over this long period. It is estimated that the population numbered up to 2.5 million animals in the 1950s. They may have been considerably more numerous than this level back when there were many more active rookeries, before the onset of exploitation by Europeans and Americans.

Northern Fur Seals compete for Walleye Pollock with one of the largest commercial fisheries world. Measurable annual mortality, especially for juveniles and subadults, is caused by entanglements in derelict and discarded fishing gear, marine debris and direct interactions with commercial fisheries. This mortality was highest during the period of active high seas drift net fishing in the North Pacific in the 1980s. But, entanglement in debris is an ongoing problem. Long-term ecosystem regime change in the North Pacific and possible changes in the foraging patterns of a key predator (the Killer Whale), may be working synergistically with the fisheries related issues to cause the current population decline.

Like all fur seals, Northern Fur Seals are vulnerable to oil spills because of their dependence on their thick pelage for thermoregulation. The small colonies at San Miguel Island in the California Channel Islands and on the Farallon Island may be at greatest risk due to proximity to major harbours, shipping lanes and offshore oil extraction facilities.

The effect of global climate change on this species is uncertain. However, any further negative disruption of the ecosystem of the northern fur seal should be considered a threat.

Small numbers of Northern Fur Seals are taken annually by Alaska Natives in a subsistence harvest on the Pribilof Islands. For the period 1999-2003, the average annual harvest was 869 animals; all animals taken were juvenile and sub-adult males. Subsistence harvest has declined in recent years to the level of 478 taken in 2007 on both Pribilof Islands (Lestenkoff and Zavadil 2007, Malavansky 2007).