Mr. Popper is a house painter in Stillwater. Admiral Drake sends Mr. Popper, one of his biggest fans, a penguin as a surprise. The penguin's name is Captain Cook and sleeps in the ice box.
Captain Cook does not seem to be doing well, so Mr. Popper contacts an aquarium. They decide that the penguin is lonely and needs a companion. With two penguins, Mr. Popper installs a freezing machine, which strains on the family budget.
Greta lays ten eggs! Usually, penguins don't lay that many, but extraordinary things happen in extraordinary circumstances. Now there will be twelve penguin mouths to feed!
The Poppers are having such a hard time paying for all of their expenses that Mr. Popper decides to train the penguins. During a successful tour of their travelling show, they arrive at the wrong theater, and the theater owner has them all arrested.
Admiral Drake pays the bail for Mr. Popper. A Hollywood movie director offers to feature the penguins in the movies. Fearing that life in Hollywood would be too much for the penguins, Mr. Popper declines.
Admiral Drake, Mr. Popper, and the penguins travel to the North Pole on an expedition to establish a penguin colony.