Jonouchi and his sister, Shizuka Jonouchi, were separated when their parents divorced. Shizuka was brought by their mother while Jonouchi lived with their father. Jonouchi lived in poverty, due to his father's gambling addictions and alcoholism.
Jonouchi became a street thug and hung out in Hirutani's gang for long periods of time when he is in middle school. He often got into fights and developed great fighting skills. He also hung out with Hiroto Honda.
Jonouchi used to pick on Yugi Mutou at school. He was annoyed by how Yugi would let himself get pushed around and claimed his bullying was teaching Yugi how to be a man and even offered Yugi to punch him back, although Yugi hates violence. He once teased Yugi by taking his box, containing the Millennium Puzzle and secretly stealing a piece. Honda tried telling Jonouchi to stop, but Jonouchi just mocked his custodian position. Anzu Mazaki took the puzzle box back and called Jonouchi a bully. To escape from Anzu, Jonouchi left with Honda as he went to queue for Miho Nosaka's lunch. In the hallway, Ushio overheard Jonouchi mentioning bullying and asked what was happening. Jonouchi tried telling Ushio to stay out of it, but was restrained by Honda, who wanted to avoid trouble. Afterwards Jonouchi showed Honda the piece of the puzzle he had taken and threw it out the window into a canal.
The next day Ushio beat-up Jonouchi and Honda, under suspicion that they were bullying Yugi. However Yugi objected and insisted that Jonouchi and Honda were his friends. On the way home, while he spoke with Honda about Ushio, Jonouchi remembered how Yugi had stuck up for him and recovered the piece of the puzzle from the canal. He then saw Ushio attacking Yugi. Jonouchi gave the piece of the puzzle to Yugi and he and Honda tried fighting Ushio off, only to get beaten-up again. However Yugi finished the Millennium Puzzle, while the three of them were barely conscious and changed to Dark Yugi, who defeated Ushio in a Shadow Game. The next day Jonouchi answered Yugi's "Something you can show, but can't see" riddle, saying it's friendship and that they're friends.
Jonouchi noticed how Anzu was acting odd, after avoiding walking home with them a few days. He initially assumes she's dating older men for pay. Miho Nosaka and later Honda investigated by followed Anzu home. Seeing them leave with Anzu the next two days, Jonouchi and Yugi followed the three of them, finding they had all gotten jobs at Burger World. There were two escaped convicts and Jonouchi assisted in identifying the first, by checking the customer's legs for a calf wound after they spilled a basket of toy cars, pretending it was an accident.