"The Girl With the White Flag" is the autobiographical account of Tomiko Higa's childhood on the war-torn island of Okinawa during World War II.

Tomiko's family has lived on the island of Okinawa for a long time. She is the youngest of nine children, and her family is well-respected because it descended from the samurai in service to the king. Tomiko's mother dies in 1944, when Tomiko is just six. Two of Tomiko's sisters are married. One brother lives on the mainland while the other is serving with the Japanese army in China.

Over the next year, her father rears her and teaches her many important things, such as how to farm, what plants to eat, and so on. He is a strict but kind man. Tomiko gets along well with her two sisters, Yoshiko and Hatsuke, and plays with her older brother, whom she calls Nini. When war does at last come to the island, their father does not return home form his duties bringing food to the military signal corps station.

Yoshiko, Hatsuke, Nini, and Tomiko decide that they will flee south at the recommendation of the army. Along the way, they encounter the horrors of war, from dead soldiers and dead civilians, to bombed-out houses and a destroyed landscape. Nini is later killed while the children spend the night on the shore. While on a road choked with refugees heading south, Tomiko becomes separated from her sisters.

She heads off on her own, scavenging for food from vegetable plots and the haversacks of dead soldiers. She meets a number of animals, and is almost killed by Japanese soldiers. Tomiko believes that God, her mother, her father, and her brother have intervened numerous times to save her life throughout her ordeal.

Eventually, Tomiko comes to stay in a cave with an elderly couple, whom she lovingly comes to call Granny and Grandpa. They help feed her, and she helps to care for them, for Granny is blind and Grandpa is a quadruple amputee. They tell Tomiko that she must go on and live a long and happy life, for her entire life is truly ahead of her. On June 25, 1945, the three hear the voices of Americans speaking in Japanese, telling the civilians to come out and that the Americans will not hurt them. The old couple make a white flag for Tomiko to carry out of the cave. She comes across three American soldiers, one of whom is taking photos. She comes to discover the Americans are kind and friendly.

Years after the war, Tomiko comes across the photo of herself and a white flag in a history book. The photo becomes well-known, and Tomiko, with the urging of her husband, writes about her experiences, and decides to seek out the soldier with the camera. She tracks him down to Texas with the help of the soldier's unit commander, and a television film crew. The photographer, John Hendrickson, is very happy to see Tomiko. He takes a photo of her with the same camera that he used forty-three years previously.