Call It Courage centers on its main character, Mafatu, a fifteen-year-old Polynesian boy. The other human characters in the story—the silent, ashamed father, the indifferent stepmother, and the mocking children—serve primarily to set the stage for Mafatu's journey.

Mafatu is the son of Tavana Nui, the Great Chief of Hikueru. Ironically, his name means Stout Heart, yet he harbors a deep fear of the ocean. This fear stems from a traumatic event when he was three years old; a violent hurricane swept him and his mother out to sea. Although his brave mother managed to get him safely to shore, she perished shortly after. The islanders feel sympathy for Mafatu, but because the sea is central to their way of life, they cannot comprehend his fear.

Consequently, Mafatu lives as an outcast, derided by the other children and pitied by his family. He yearns to fish with the other boys but is unable to overcome his terror. When he realizes his beloved father is deeply ashamed of him, he finally succumbs to the taunts of the other boys. On an impulse, he sets off to sea in a small outrigger canoe.

Mafatu's loyal companion is a small yellow dog named Uri. Uri adores Mafatu, accompanying him on every step of his journey and motivating him to persevere. Uri relies entirely on Mafatu, and Mafatu often attempts feats for Uri's sake that he would never try for himself. Uri gives Mafatu a reason to be brave.

During his journey, Mafatu encounters Kivi, an albatross with a crippled leg, and rescues him from other birds. He nurses Kivi back to health, and eventually, the bird takes flight but never forgets Mafatu's kindness. In Mafatu's darkest moments, Kivi reappears overhead, offering comfort. Mafatu, Uri, and Kivi are all outcasts in their own ways.

As the story unfolds, Mafatu matures and gains confidence by overcoming numerous challenges. He braves the sea and wind and faces the island's dangers, including the feared "eaters of men." He builds self-assurance by using his skills to provide food and shelter for himself and Uri. In a triumphant moment, he laughs in the face of the fearsome sea god, knowing he cannot be defeated. His heroic actions, showcasing various forms of courage, bolster his self-esteem. When Mafatu finally returns home, he is gaunt from his ordeal but can hold his head high. Courage shines in his eyes. His father is almost unable to recognize him, and the islanders welcome him as a full member of the community.