Animals at the zoo include Mandarin ducks, cranes, red pandas, chimpanzees, hamadryas baboons, reptiles, lion, tigers, tanuki (raccoon dogs), badgers, pheasants, love birds, zebras, giraffes, flamingos, camels, ruffed lemurs, white-mantled black colobus, black-capped capuchins, swans, ducks, kagus, penguins, wallaby, deer, eagles, owls, condors, bears, and Tokyo bitterlings.

[4] The red panda is one of the first animals visitors see upon entering the zoo, and also one of the most popular.

[6] It is primarily home to small animals such as mice, guinea pigs, chickens, and fantail pigeons,[7] and snakes.

[5] The Nogeyama Zoo was the first zoo in Japan to successfully house leopards (1952), blackbuck (1953), dromedary (1954), sloth bear (1965), ring-tailed lemur (1969), pileated gibbon and caracal (1974), clouded leopard (1983), giant anteater (1985), Kleinmann's tortoise (1992), Asian forest tortoise (1997), and radiated tortoise (2009).

It was also the second zoo in the world to successful breed Andean condors in captivity in 1972.