Mr. Popper paints houses in Stillwater. He lives with his family which is a wife, his daughter Janie, and his son, Bill. He dreams about faraway places, and he writes to the great Admiral Drake. The Admiral writes back and gives him a surprise- a real penguin, which he names Captain Cook.
Captain Cook lives in an icebox. He grows, but his health is deteriorating. He writes to an aquarium, who also has a female penguin in the same condition. Mr. Popper gets sent the other penguin, named Greta. Captain Cook and Greta are happy together, and they live together. However, both cannot fit into an icebox, so Mr. Popper opens the window so that the winter breeze will fill the house. Mr. Popper eventually has someone build a freezing plant in the basement. As he is only a painter, he does not have a lot of money, and this is hard for them.
Greta starts to lay eggs. She lays eggs once every 3 days. In the end, they have 10 babies, making 12 penguins total. They must strain to feed every penguin.
Mr. Popper and his family raise money by training the penguins, where they act in circuses. Mr. Popper's penguins cause havoc, and they were in the wrong theater. The conductor has them thrown into jail. Admiral Drake pays bail for them, and together, they decide that the penguins must go to the North Pole with Admiral Drake. Mr. Popper is devastated until Admiral Drake invites him to go to the North Pole with him.
In the end, he goes and promises to be back in a few years.