In Dragon Ball GT, Goku undergoes a significant physical transformation that drives the plot of the series. Approximately five years after the conclusion of the battle with Majin Buu, during a confrontation with Emperor Pilaf, a wish made on the Black Star Dragon Balls accidentally reverts Goku to the physical appearance of a child. Despite this youthful form, Goku is chronologically in his early fifties, though his Saiyan biology means he ages slower than humans. He retains his spiky black hair, defined musculature even in his smaller frame, and his Saiyan tail, which has regrown and becomes a key aspect of his later transformations.

Personality-wise, this version of Goku remains the same pure-hearted and cheerful martial artist he has always been. His innocence and lack of malice allow him to ride the Kinto'un and use techniques like the Genki Dama. However, the journey brings out his more serious and responsible side as he faces the consequences of his friends' actions. He is not as naive as he was in his original childhood, possessing decades of battle experience, wisdom, and the strategic mind of a seasoned warrior. His primary motivation shifts slightly from simply seeking stronger opponents to protecting the Earth from a ticking clock. Because the Black Star Dragon Balls scattered across the galaxy after the wish, Goku must venture into space to retrieve them all within one year; if he fails, the negative energy released from the wish will cause the Earth to explode. This mission rekindles the series original sense of adventure, forcing him to explore strange new worlds.

In the story, Goku serves as the central anchor of the Dragon Team. He is accompanied by his granddaughter, Pan, and the teenage son of Vegeta, Trunks. His role is not just that of a powerful fighter but the leader of this space expedition. He has a close and teaching-oriented relationship with Pan, often acting as her mentor and protector, though her stubbornness frequently leads to conflict. He retains his iconic rivalry and respect for Vegeta, who remains on Earth. His relationship with his wife, Chi-Chi, is strained by his sudden departure and reverted age, but she remains a background motivator for him to return home safely.

Gokus character development in GT is reflective and physical. Having already achieved various Super Saiyan states in Dragon Ball Z, he discovers a new pinnacle of power. By utilizing his regrown tail, he can transform into a Golden Great Ape when exposed to Blutz Waves, a form that combines the raw power of the Oozaru. Regaining his senses within this form allows him to achieve Super Saiyan 4. This form reverts him to an adult physique, covers his torso in red fur, and grants him immense power, representing a mastery of both his primal Saiyan instincts and his disciplined martial arts training. Despite his power, his child body has difficulty maintaining the strain of Super Saiyan 3, making this new form a necessary evolution. He also wields the Nyoibo, or Power Pole, a keepsake from his grandfather that proves useful during his adventures.

Notable abilities in Dragon Ball GT include several unique variations of his classic techniques. As a Super Saiyan 4, he frequently employs the 10x Kamehameha, which is ten times more powerful than the standard version. He also masters the Ryuken, or Dragon Fist, a devastating physical strike that manifests the energy of a golden dragon to pierce through opponents. In one instance, while trapped in a collapsing pocket dimension called Sugoroku Space, Goku demonstrates his overwhelming power by firing a Kamehameha strong enough to tear a hole in the fabric of that reality, allowing him to escape. By the end of the series, his power reaches its apex when he absorbs the Dragon Balls themselves to deliver the final blow to Omega Shenron, the shadow dragon. Following this ultimate battle, Goku departs from Earth on the back of the original Shenron. Centuries later, he is briefly seen watching over his descendants at a martial arts tournament, suggesting he achieved a form of apotheosis or ascended beyond the mortal plane.