In Omaha, Nebraska, Father Flanagan (Spencer Tracy) runs a soup kitchen for homeless men, but finds the urchins of the city need his help. When Skinny (Martin Spellman) finds himself in trouble for running with a bad crowd, Flanagan intervenes and tells a judge he will take a gang of wayward boys under his guardianship. With a friend’s donation (Henry Hull), he takes an abandoned house and begins taking in homeless children. Soon the house becomes too small, and Flanagan looks for a parcel of land out in the country to build a small complex of houses, to be run as an independent city, by the boys. Years later, a convict asks him to take in his little brother Whitey Marsh (Mickey Rooney) who becomes Flanagan’s greatest challenge. Whitey hates Flanagan and all the boys he meets, especially the young Mayor Freddie (Frankie Thomas). Whitey finds friends by Pee Wee (Bobs Watson) and Tony (Gene Reynolds), but his hostility leads to a big fight with Freddie in the ring and Whitey leaving “Boys Town.” He is drawn back to his brother’s criminal gang and requires Father Flanagan to step back into the picture to save the day.