- Mason (Conrad Vernon) and Phil are two intelligent chimpanzees. Mason can speak but cannot read; Phil is mute but is an avid reader, and communicates through sign language which is interpreted by Mason.
- Alice (Mary Scheer) is a surly zookeeper, who regularly expresses disinterest in her job. Though another worker can sometimes be heard on her walkie-talkie, and seen working around the zoo, his face is never seen.
- The Rat King (Diedrich Bader) is a genetically enhanced, muscular lab rat who resides in the sewers. He is a secondary antagonist to the penguins. He constantly torments the penguins and never learns his lesson when he is defeated each time, although his raw strength often requires them to resort to less direct measures to defeat him. He even tries to take over their home, but is beaten by King Julien in an ice hockey game.
- Roger (Richard Kind) is the penguins' alligator friend who lives in the sewer. They meet him in the episode "Haunted Habitat" when Skipper and Marlene go to investigate in the sewer under Marlene's habitat because of a strange sound. Roger tells the penguins that he is from Florida. He appears again in "Roger Dodger" when the sewer rats terrorize him and in "Gator Watch" when he wants a new home, eventually being captured and sent to the zoo.
- Max (Wayne Knight) is the penguins' stray cat friend. He first meets the four penguins in the episode "Launchtime" when the penguins end up on a rooftop across the street from the zoo instead of on the moon. At first, the penguins thought he was a "moon-cat" but at the end they figure out he was a stray cat, but they still refer to Max as "Moon-cat" out of habit. Max is skinny and hopes to catch a bird in his life. He at first wanted to eat the penguins, but was so touched that he was given a can of fish by them that he became their friend instead. He appeared again in "Cat's Cradle", in which he tried to hide from Officer X from Animal Control.
- Joey (James Patrick Stuart) is an ill-tempered kangaroo with an Australian accent. He has fought other characters on the show.
- Bada and Bing (John DiMaggio and Kevin Michael Richardson) are two gorillas who enjoy fighting. They once beat up Mort, which led to Mort growing after he was thrown into Kowalski's latest invention, and they then got beat up by Mort to get a mango. Julien once gave them lots of bananas but it is possible that they beat him up due to him giving too much to them.
- Fred (Fred Stoller) is a squirrel that takes everything said literally and has a slow monotone speech pattern. Fred lives in a park near the zoo. He dated Marlene in "Otter Things Have Happened", but she broke up with him.
- Officer X (Cedric Yarbrough) is an officer in animal control. He is obsessed with catching stray animals. He has a stronger grudge against the penguins than Alice. His first appearance is when he is searching for Max and the second appearance is when he was tracking down the penguins when they escaped the zoo. He is a very strong man and can take down even the strongest of animals, like Joey the Kangaroo. Officer X is very cocky and seems to have hunted many other animals before. In his second appearance he was arrested for going on a rampage after losing the penguins. He was an exterminator hired to remove cockroaches that Rico had befriended in "Stop Bugging Me" and a temporary zookeeper when Alice went on vacation in "The Officer X Factor". In the episode "A kipper for Skipper" he is shown to be a fishmonger and manages to capture Kowalski, Private and Rico. But as in the other times they manage to escape, even though he was close to catch Kowalski in his obsession. And again he gets trouble with the law.
- Dr. Blowhole (Neil Patrick Harris) is Skipper's archenemy. He is a bottlenose dolphin who has red lobsters as servants. He was mentioned in the episodes "Eclipsed" and "Roomies", but he makes a full appearance in the special "Dr. Blowhole's Revenge", where he captures Julien and served as the primary antagonist of the episode (He was also referenced in "Invention Intervention", when Skipper believed that Kowalski's out-of-control invisible invisibility ray was Blowhole's creation, although Skipper also noted that disintegration was more Blowhole's style). Doctor Blowhole also makes a full appearance in "The Return of the Revenge of Doctor Blowhole", when he uses his "Mind Jacker" and "Diaboligizer" to take over Central Park Zoo, but transforms Julian's Mp3 player into a giant "music monster". In "The Penguin Who Loved Me", a sequel episode to "The Return of the Revenge of Doctor Blowhole", having had his memory erased by his own Mind Jacker, Blowhole remembers himself as Flippy, "Seaville's second most popular performer". He recalls nothing of the penguins or his evil self. In this episode his nameis revealed to be Francis, and has a sister named Doris. He rides on a Segway-type vehicle as his means of transportation on land. Four running gags are that his skin is "surprisingly pleasant to the touch", that he constantly mispronounces "penguins" as "peng-u-ins", that he calls the penguins "flightless", and that he constantly rubs in the fact that he has far more superior technology than the penguins do.
- Burt (John DiMaggio) is an elephant who was just one of the extra animals during the beginning of the series, but then he evolved into a character later on and even got a central episode in "An Elephant Never Forgets". He is shown to be obsessed with peanuts.
- Manfredi and Johnson are two unseen recruits, referenced mainly by Skipper, who have suffered horrible, seemingly fatal ("You know, one up there and one down there!" –Skipper.) events in a number of previous penguin missions. Their "fates" have included having been attacked by "flying piranhas", their remains later ladled into their graves with a teaspoon; having been short one escape tunnel, their remains later sent back in a manila envelope, coincidentally from Manila; having mistook the "business end" of a beluga for an escape tunnel, resulting in them not being able to speak for months; having fallen for the "exploding elephant foot trick"; a Chinese lantern and six bottles of rocket fuel for a talent show; having lost their hearts, a lung, and 15 feet of intestine when they fell in love with two Chinstrap sisters; and being apparently literally smothered when a message informing the others to smother them with affection was misinterpreted. The two make a brief appearance—alive—in the episode "The Penguin Who Loved Me". "Manfredi" and "Johnson" are also the names of the two American POWs killed while trying to escape the German prison camp in the 1953 movie Stalag 17.
- Hans (John DiMaggio) is a puffin with a past history with Skipper that involves a mission in Denmark that somehow resulted in Skipper being declared Public Enemy Number One in the country in question. During "Huffin & Puffin", he appeared in New York, initially apparently wanting to make peace with Skipper, before his true agenda was revealed to be his attempt to take control of the Penguins' lair for revenge. With Skipper having infiltrated the lair and defeated Hans, he was then shipped to the Hoboken Zoo. He appeared in "The Return of the Revenge of Doctor Blowhole", working with Doctor Blowhole as part of a plan to take Skipper's memories.
- Eggy (Tara Strong) is a duckling who the penguins once "egg-sitted" in "Paternal Egg-Stinct". In the episode "Hard Boiled Eggy", the penguins learn that because they influenced him while inside the egg, Eggy had all their commando strengths combined. At the end of the episode, Julien teaches Eggy how to dance and Eggy finds such better than trying to be a penguin.
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Famous quotes containing the words characters and/or secondary:
“His leanings were strictly lyrical, descriptions of nature and emotions came to him with surprising facility, but on the other hand he had a lot of trouble with routine items, such as, for instance, the opening and closing of doors, or shaking hands when there were numerous characters in a room, and one person or two persons saluted many people.”
—Vladimir Nabokov (18991977)
“Cloud-clown, blue painter, sun as horn,
Hill-scholar, man that never is,
The bad-bespoken lacker,
Ancestor of Narcissus, prince
Of the secondary men. There are no rocks
And stones, only this imager.”
—Wallace Stevens (18791955)