Mr. Popper is an unkempt house painter who dreams about Polar expeditions. He spends all of his free time reading about the Poles and the explorers who visit them. He tenderly talks about the penguins at the South Pole and wishes to have one as a pet. Unlike carefree Mr. Popper, Mrs. Popper is very worried about having enough money to get through the winter, and keeping a clean house. Excitedly, Mr. Popper realizes the date, and rushes to turn on the radio. He hears Admiral Drake, an explorer in the Antarctic, saying hello and warning him of a surprise.
It doesn’t take too long for Mr. Popper to find out his surprise; the next afternoon, while Mrs. Popper was out, a large package gets delivered to the door. Inside is a penguin from Antarctica, whom Mr. Popper decides to name Captain Cook after the famous English explorer.
Captain Cook explores the living room, the refrigerator, and the dining room. Mr. and Mrs. Popper and the children, Bill and Janie, watch and wonder if Captain Cook is hungry and where he will sleep. Mr. Popper clears out a space in the icebox, being sure to leave the door open for air and ice cubes on the bottom to replace rocks.
The next day, Mr. Popper pays a serviceman to work on the icebox. He asks the man to drill holes in the icebox and to install a handle on the inside. The serviceman thinks he is crazy, but after being handed a five dollar bill, does the work. With the new modifications, Captain Cook is able to enter and exit the icebox on his own.
Captain Cook is very mischievous in this new setting, which results in some mayhem. First, a policeman knocks on the door to inspect the new pet; he determines that Captain Cook seems friendly enough, but he should remain indoors, and suggests that Mr. Popper call the City Hall to see if he needs a license. While the Poppers are busy, Captain Cook collects dozens of miscellaneous items from around the house and puts them in his icebox. While out for a walk with Captain Cook, news reporters interview Mr. Popper and take their picture, which appears in the newspaper the next day.
Soon, Captain Cook becomes very ill; everyone in the town tries to help, but he just continues to decline. Mr. Popper writes a letter to Dr. Smith, the Curator of the great Aquarium in Mammoth City. Dr. Smith replies that he, too, has a sick penguin and believes it is due to loneliness, so he is going to send his penguin, Greta, to Mr. Popper. The two lonely penguins quickly recover.
As the weather gets colder, Mr. Popper decides to leave the windows open for the penguins, forcing the family to wear their coats in the house. When snow ends up in the house, Mr. Popper decides to fill the house with water to make ice, allowing the penguins and kids to toboggan around the living room. Mrs. Popper is unhappy with the mess and tells Mr. Popper to figure something else out.
Mr. Popper then installs a freezing plant in the cellar and moves the penguins. Just as Mrs. Popper had predicted, Greta lays ten eggs just a few days after being moved. Mr. Popper digs a hole in the cellar to make a swimming pool for all the penguins and an ice tower for them to climb on. Mr. Popper, Bill, and Janie spend hours just watching the penguins; Mr. Popper dreads having to go back to painting houses in the spring.
Mrs. Popper discusses money with Mr. Popper; they don’t have enough money to pay the bills and the penguins are very expensive. They come up with an idea to teach the penguins to do tricks and perform in the theater. After some practicing, Mr. Popper’s family and the ten penguins walk to see Mr. Greenbaum, the owner of the Palace Theater, to show him the act. The act is a huge success; they travel across the United States performing in all the big cities and are paid $5,000 a week. Toward the end of the tour, Mrs. Popper and the penguins are very tired of performing, and Mrs. Popper wants to return to Stillwater.
Before she can return, there is a mix-up between the Regal and Royal theaters in New York, and Mr. Popper winds up in jail with his twelve penguins. Admiral Drake from the South Pole bails him out, and is thrilled with everything Mr. Popper has taught the penguins. Admiral Drake offers to take the penguins to the North Pole to give the explorers company, but Mr. Klein, owner of the Colossal Film Company, offers to make the Poppers a fortune by filming the penguins in Hollywood. Mr. Popper takes the evening to make his decision, but ultimately decides the penguins will be much happier in the North Pole. Mr. Klein understands, but decides to shoot a short film about the penguins before they leave for the North Pole, paying the Poppers twenty-five thousand dollars.
Mr. Popper says goodbye to all the penguins as they board the ship; he wipes the tears from his eyes as he says goodbye to Captain Cook. He then says goodbye to Admiral Drake who is surprised, asking, “Aren’t you coming with us?” At this, Mr. Popper asks Mrs. Popper if she would mind if he went to the North Pole for a few years. Mrs. Popper agrees, wishing him good luck on his next adventure.