Call It Courage has one main character, Mafatu, a fifteen-year-old Polynesian boy. Other human characters in the book—the silent, ashamed father, the uncaring stepmother, and the teasing and scornful children—simply set the mood in preparation for Mafatu's journey.

Mafatu is the son of Tavana Nui, the Great Chief of Hikueru. Mafatu's name, ironically, means Stout Heart, yet he fears the ocean because when he was three years old, a dreadful hurricane swept him and his mother out to sea. After getting him safely to shore, his courageous mother died. The islanders sympathize with Mafatu, but the sea is their entire livelihood; they do not understand how one can be afraid of the sea.

So Mafatu lives as an outcast, scorned by the other children and pitied by his family. He desperately wants to fish with the other boys but cannot conquer his fear. When he realizes that his father, whom he loves dearly, is utterly ashamed of him, he finally allows himself to be goaded into action by the other boys. Impulsively, he sets out to sea in a small outrigger canoe.

Mafatu's constant companion is a small yellow dog named Uri. Uri worships Mafatu, follows him on every step of his journey, and encourages his master to succeed. Uri depends completely on Mafatu, and repeatedly Mafatu attempts deeds for Uri's sake that he would never have tried for himself. Uri gives Mafatu a reason to find courage.

Mafatu also meets Kivi, an albatross with one defective leg, and saves him from the other birds. He nurses Kivi to recovery, and one day the bird soars off. But he never forgets what Mafatu did for him. When things are at their worst for Mafatu, Kivi appears overhead as a comforting presence. Mafatu, Uri, and Kivi are all outcasts, each in his own way.

As the story progresses, Mafatu grows and matures as he overcomes successive obstacles. He defies the sea and wind and confronts the dangers of the island, including the dreaded "eaters of men." He develops self-confidence by using his skills to provide food and shelter for himself and Uri. At his triumphant moment he laughs in the face of the terrible sea god, knowing he cannot be defeated. His heroic deeds, which reveal the many faces of courage, build his self-esteem. When Mafatu finally returns home, he is gaunt from his ordeal but he can hold his head high. Courage blazes from his eyes. His father can scarcely believe that this is his own son, and the people of the island accept him as a full member of the community