The Juan Fernández Fur Seal is a polygynous species. Based on sealer observations made during the late 18th century, the breeding season lasts from mid-November through the end of January, and the colonies are essentially vacated by early September, and no later than mid-October (Francis et al. 1998).

Juan Fernández Fur Seals are sexually dimorphic from the time of birth (Osman et al. 2010) and the differences in length and weight increase with age. Adult males reach 2 m length and weigh 140 kg. Lactating females are on average 1.42 m in length and 48.1 kg in weight (Francis et al. 1998). Newborn pups are approximately 65-68 cm long and weigh 6.2-6.9 kg, and are born with a black coat. Male pups are significantly larger and heavier than female pups at birth, but they do not grow faster than females nor do they show significant differences in body condition. Differences in the growth rates of male and female Juan Fernández Fur Seal pups appear to originate before birth and are not accentuated during the nursing period (Osman et al. 2010).

Males defend territories on land that typically cover about 36 m² and that include an average of four females; some males also hold larger territories in the water (Francis et al. 1998). Most adult females give birth within a few days of arriving at the rookery. Mean time from birth to the first foraging trip is 11.3 days. Although females can be gone for as little as a day, the mean length of foraging trips is 12.3 days, with the longest recorded trip lasting 25 days. Mean duration of pup attendance between foraging trips is 5.3 days with a range of 0.3–15.8 days. Based on the onset of pupping and the observations at vacant colonies in early September, pups appear to be weaned at 7-10 months old (Francis et al. 1998).

Juan Fernández Fur Seal females travel long distances to find adequate quantities of prey making some of the longest foraging trips of any otariid (Francis et al. 1998, Osman 2007). Most trips were made to the southwest and west of the Juan Fernández Islands, far offshore, to deep oceanic areas more than 550 km from the island (mean = 653 km) and up to 889 km distant. The mean dive depth was only 12.3 m and the mean dive duration was 51 seconds, suggesting mostly surface feeding (Francis et al. 1998). Osman (2007) analysed 27,541 dives made by five females from Alejandro Selkirk Island during a single foraging trip, obtaining a median dive depth of 4 m and median dive duration of 0.33 minutes. Maximum depth attained by any seal was 169.5 m during a dive lasting 3.1 minutes and the longest dive lasted 5.1 minutes with a maximum depth of 24 m. The median maximum depths ranged from 3.5 m to 4.5 m (Osman 2007). Francis et al. (1998) reported that nearly all foraging-type dives occur at night; however (Osman 2007) found feeding during daytime to be more frequent.

Juan Fernández Fur Seals feed extensively on vertically-migrating prey (Francis et al. 1998). Their diet is one of the least diverse of any otariid. Coupled with the long foraging trips made by lactating females, this pattern reflects the low productivity of their oceanic feeding areas (Acuña and Francis 1995). The diet composition of Juan Fernández Fur Seals was assessed by analysing 437 scats collected during five reproductive seasons (1987–1991). The study yielded 4,172 fish otoliths and cephalopod beaks, with 13 prey species identified. Myctophidae represented most of the items (80.3%), followed by Scomberesocidae (10%), Carangidae (9.5%), Engraulidae (1.0%), and Bathylagidae (0.7%). Cephalopod families included Onychoteuthidae (27.1%), Ommastrephidae (3.7%), and Tremoctopodidae (0.7%) (Acuña and Francis 1995). Scat samples from females contained larger numbers of the Squid Onychoteuthis banksi than did the samples from subadult males and juveniles.

Two-thirds of the 60 Juan Fernández Fur Seal pups found dead on Alejandro Selkirk Island during the 1991 and 1992 breeding seasons had Hookworms (Uncinaria sp.), with a mean infection of 17 parasites per host (Sepúlveda 1998). Blue Sharks, Great White Sharks, and Killer Whales are suspected predators, and Leopard Seals that infrequently visit the islands may also prey on Juan Fernández Fur Seals (Torres 1987).

Juan Fernández Fur Seals inhabit three islands in the Juan Fernández Archipelago (Alejandro Selkirk, Robinson Crusoe, and Santa Clara Islands) as well as the San Félix Islands (San Félix and San Ambrosio), also called “Islas Desventuradas”. The Juan Fernández Islands are located approximately 650 km west of Valparaiso, off the Chilean coast. The San Félix Islands are located approximately 910 km due west of the Bahia Chanaral de Las Animas on the coast of Chile´s Atacama Desert. Almost the entire population resides on the Juan Fernández Archipelago, with very few animals being found on the San Felix Islands (Osman 2007, National Geographic-Oceana 2013). The Robinson Crusoe (47.9 km²) and Alejandro Selkirk (49.5 km²) Islands are the largest and are home to the majority of the population (Osman 2007). The San Félix Islands are much smaller: San Ambrosio measures 2.2 km² while San Félix covers 1.4 km².

In 1990 and 1991, five adult female Juan Fernández Fur Seals from Alejandro Selkirk Island were instrumented with satellite transmitters that indicate they made foraging trips primarily south and west of the archipelago to locations up to 889 km away, with all tracked females at some time located over 550 km from the island (mean = 653 km; Francis et al. 1998). In another study conducted in 2005 (Osman 2007), satellite locations from seven instrumented adult females indicated some animals foraged near the Juan Fernández Archipelago while others travelled as far as 837 km toward the coast of Chile, reaching the continental shelf near Concepción Bay. The mean distance ravelled offshore by female Juan Fernández Fur Seals was 1,394 km. Juan Fernández Fur Seals have been sighted with regularity since 1983 at Punta San Juan, Perú (Majluf and Reyes 1989) which is considered here as the northern limit of their extent of occurrence. However, the northernmost record for the species comes from a vagrant male sighted on the San Francisco beach in Buenaventura Port, Colombia (3°53’N, 77°4’W; Avila et al. 2014). The southern limit is represented by the farthest distance recorded for instrumented animals from Alejandro Selkirk Island approximately 890 km to the southeast (Francis et al. 1998).

Hunting of Juan Fernández Fur Seals has been prohibited since 1965 (Aguayo 1979). In 1978, the status of total protection was conferred to all Arctocephalus species in Chile (Torres 1987, Reijnders et al. 1993).