Juan Fernandez fur seals are sexually dimorphic, with males about 1.4 times longer and approximately 3 times heavier than adult females.  Juan Fernandez fur seals have thick pelage, with dense underfur.   Adults have moderate length whitish-cream vibrissae and long prominent ear pinnae.

Adult males have a rounded crown with the apex above the ear pinnae.  There is a slight rounded forehead where the crown meets the base of muzzle. The muzzle is long, straight, somewhat flattened on top, and tapers in width and thickness to the fleshy nose on the end.  The black naked skin of the nose, or rhinarium, is large and somewhat bulbous and the nares orient downward.  The large rhinarium gives the muzzle a slight upturned look at the end, especially in males.  The mane extends to the crown, and the long erect guard hairs on the head accentuate the crown and forehead.  This is especially noticeable where the longer fur of the crown meets the shorter, more swept-back, fur of the muzzle between the eyes.  From the crown, the long coarse guard hairs of the mane cover the nape and neck to the shoulders, and on the sides and undersides of the neck from throat to chest.  The neck, chest and shoulders to the fore flippers are enlarged with muscle and fat.  The abdomen is much smaller, and tapers to the narrow pelvis.  The canine teeth of adult males are larger and thicker than those of females.

Adult females, subadults, and juveniles also have a long tapering muzzle, with nares angled slightly downward.  However, because the rhinarium is not enlarged, the muzzle is more pointed. The crown is slightly domed, giving the head a rounded look in profile.  The ear pinnae are long and stand out from the head enough to make them conspicuous.  The mane is absent and the neck and shoulders are in proportion with the rest of the body.

The fore flippers have a dark, sparse, short fur that extends beyond the wrist onto the middle of the dorsal surface of the flipper in a “V” pattern that does not reach the rounded tip.  The rest of the dorsal surface, and the palms of both fore flippers are covered with a hairless black leathery skin.  The first digit is the longest, widest and thickest, and curves posteriorly, giving the flipper a swept-back look.  Digits 2-5 are successively shorter.  There is a small opening in the skin at the end of each digit for a claw that is usually reduced to a vestigial nodule, and rarely emerges above the skin.  The claw openings are set back from the free edge of the flippers by cartilaginous rods that extend the length of each digit, and expand the size of the flippers.

The hind flippers have dark, short, sparse hair covering part of the proximal end of the flipper, and the rest of the dorsal surface, and the entire sole is covered in black leathery hairless skin.  The hind flippers are long and each digit has a cartilaginous rod that adds a flap-like extension to each toe.  The bones of the three central toes terminate at the position of the small nails that emerge through the skin on the dorsal surface, set back from the end of the flipper.  The claws of digits 1 and 5 are vestigial, like the claws on the fore flippers, and may or may not emerge from small openings set back from the end of the flaps.  All of the flaps at the end of the flipper are of relatively equal length.  The first toe or hallux and the fifth toe are somewhat wider than toes 2–4.

Coloration of adult males is dark grayish brown to grayish black.  The longer guard hairs of the mane are light tipped off-white to ginger on the crown, nape and, to a variable extent, on the sides and back of the neck, creating a grizzled appearance.  Adult males have scars from fighting, and some are heavily scarred.  Adult females, subadults, and juveniles are dark brown to grayish-black above and paler in variable patterns below, especially on the chest and underside of the neck, which can be tan to creamy gray.  Both sexes have a variable amount of lighter buff to reddish brown color on the muzzle, which often extends into the face above the eyes.  Pups are born in a black wooly coat.

Adult males are estimated to be 2 m long and weigh 140 kg.   A series of lactating females, combined from several years, were an average of 1.42 m long and weighed an average of 48.1 kg.  Newborn pups are approximately 65-68 cm and 6.2-6.9 kg.

The dental formula is I 3/2, C 1/1, PC 6/5.

South American, Antarctic, and Subantarctic fur seals, and South American sea lions have distributions that bring them near to the range of Juan Fernandez fur seals.  Subantarctic and Antarctic fur seals have been recorded from the Juan Fernandez Islands, and Juan Fernandez fur seals occur as vagrants along the coast of Chile.

Adult male Juan Fernandez fur seals have a longer muzzle, distinctive bulbous rhinarium, and unique coloration of the crown, nape and upper neck that separate them from Antarctic and South American fur seals.  Separating adult female, subadult, and juvenile southern fur seal species at a distance is usually difficult and often impossible without extensive experience with the species in question.  In general, adult female Juan Fernandez fur seals are longer and heavier than female Antarctic, Subantarctic, and South American fur seals, and have downward oriented nares, and a more rounded crown.

Subantarctic fur seals are uniquely colored.  The back and rump of adult males is dark gray to brownish black, and the chest and neck through the muzzle, face and area around the eyes are cream with yellow to orange shading.  The ear pinnae are short, mostly bare skin and dark, and attach in the dark pelage of the upperparts.  There is also a tuft of longer pale fur in the dark crown above the eyes and behind the dark forehead.  Although the adult male is enlarged and thick in the shoulders and neck, he does not have a mane.   Adult females have similar coloration to the males, but have less well-defined pale facial markings that can be shaded with dull yellow orange to light brown.  In both sexes the top of the fore flippers is darker as is the area where the flippers attach to the sides.  The underside of the abdomen is dark ginger to reddish brown.  The fore flippers and hind flippers are proportionately short and wide.

South American sea lions have large, blocky heads with a short muzzle that is blunt on the end, and smallish inconspicuous ear pinnae.  They are also pale tan to light golden brown, with sleek fur that is not dense or shaggy, except in the case of the mane on the otherwise unmistakable adult males, and are heavy bodied.