Juan Fernandez Fur Seals were hunted to the brink of extinction by commercial sealers trading pelts in China. Intensive sealing began in the late 18th century and ended in the late 19th century, when few could be found. It is likely that several million Juan Fernandez Fur Seals were killed during this period. Small numbers were seen in the early 20th century, but the species was thought to have gone extinct shortly thereafter. The species was rediscovered in the middle of the 20th century and has since been making a slow comeback.

The limited size of the population and the fact that the species passed through a genetic bottleneck makes this species vulnerable to catastrophic events and stress from disease outbreaks, oil spills, environmental regime shift, disturbance, and fisheries conflicts. No fisheries conflicts have been identified to date. Individual seals have been seen with plastic bands around their necks since 1982, but the level of mortality from these entanglements is unknown.

The effects of global climate change on this species are uncertain; however, any negative disruption of the ecosystem of this species, that already undertakes some of the longest foraging trips during the pup dependency period, would likely be a threat.