The song tells the preposterous, yet moving, tale of a young man's quest for revenge on an absent father, whose only contribution to his entire life was naming him Sue, commonly a feminine name, which regularly resulted in the young man suffering from ridicule and bullying.
Sue would later find his father and confront him, resulting in a vicious brawl. After the two have beaten each other almost senseless, Sue's father admits that the name was given to him as an act of love: because he knew he would not be there for his son, Sue's father gave him that name to make sure that he grew up strong. Learning this, Sue forgives his father and they have an emotional reconciliation.
With his lesson learned, Sue closes the song with an announcement: "And if I ever have a son, I think I'm gonna name him . . . Bill or George, any damn thing but Sue! I still hate that name!"
The song is mostly recitation rather than conventional singing, an early form of rap.
Years later, songwriter Silverstein wrote a follow-up named "The Father of a Boy Named Sue" in which he tells the old man's point of view of the story.