Gon is a young boy with long spiky black green tipped hair and large, hazel brown eyes. His usual outfit is composed of a green jacket with reddish edges covering a black or white tank top underneath, green short shorts, and green, laced boots. In some arcs such as the Greed Island and Chimera Ant arcs he takes off the jacket and wears only the tank top. In the Greed Island arc and at the beginning of the Chimera Ant arc he wears the Paladin's Necklace, a Greed Island card with the ability to purge any external effects to a card the wearer is holding.

Gon is an athletic, rustic, and friendly boy who is searching for adventure. Also, he is not very good at math. However, having spent a lot of time in the woods as a child, he is very good with animals. Gon is an Enhancer, who are known for being simple-minded and determined. This determination and talent leads to both potential allies and potential enemies trusting in him and taking his side. He has inhuman senses; Gon has a heightened sense of smell almost like a dog's, he also has very good vision, as well as having very keen taste. Gon wants to become a Hunter because he wishes to find out the depths of an occupation that would cause a father to choose the profession over being with his own son.

Simultaneously, his flaws lie in his temper and impulsive nature. Gon sometimes fails to think things through and such actions lead to him suffering. Though possessing talent far beyond the norm for his age, anytime his abilities are challenged, he feels as if he has to prove his antagonist wrong.

He continually strives to obtain greater power, often becoming exceptionally stronger in his anger. But Gon's anger also leads to some extremely reckless tendencies. When his emotions are ignited, Gon becomes irrational and completely oblivious to anything else. While his will is stronger than most and he can be very level-headed, this clear mind can also make him very cold at times. When Gon is cool-headed, it is shown that he can think very creatively and thoughtful to solve a problem. The prime example is in the third stage of the Hunter Exam in which he can think clearly enough under heavy stress to find the way to get through the lock door to the finish line with all his companions by breaking the wall to lead to the finish line in time, which is the feat not even level-headed people like Kurapika or Killua can think of.

Often it is difficult for others to understand or relate Gon's actions or thoughts to what people would consider "normal" thinking, with some believing him to be a little insane. Zepile remarked on how Gon "doesn't care about the good or the bad" when he is curious or amazed.[6] His morality is complex, almost juridical: Gon values life and ethics, but he can dissociate his personal feelings from them. He thanked Binolt, a serial killer, after he helped him get stronger,[7] and, in spite of being aware of how dangerous he is, Gon admires Hisoka for his might. Despite wanting to put a stop to the actions of the Phantom Troupe, Gon never hated them until he discovered they were capable of feeling emotion and empathy.[8] He never judged Killua for his past as an assassin, but he snapped at Illumi when he started to suspect that, rather than Killua killing because he was not taught to value life, his family was forcing him to do so regardless of how he felt about it.[9] Notably, however, he did not even think about warning Agon when the latter was about to cross paths with Hisoka, despite knowing fully well that the encounter would inevitably result in the man's death, all for the sake of obtaining the magician's tag.

When Kite died facing Neferpitou, Gon blamed himself for being too weak and entered a destructive and self-destructive spiral. At the apex of his mental breakdown he was willing to kill Komugi if Neferpitou did not accept his request, and ultimately accepted to give up his own life to kill the Ant.

Gon is extremely confident in his abilities. Sometimes, he does not realize when the opponent is far stronger or even after he knows the opponent is stronger than him; regardless, he will continue to fight. He refuses to accept himself as inferior to any opponent that he disagrees with, including those clearly stronger than him. Togashi initially portrays this as naïveté. Aside from becoming a Hunter and finding his father, Gon desires strength above all else. Gon's greatest insecurity lies in his own weakness and not being able to protect those who are closest to him.

A running gag in the series is that he often has problem with math and numbers. The prime example is he miscalculates the weight of the challenge doors at Zoldyck's estate until Kurapika has to correct him or he misreads the price tag as five hundred, eighty million and Killua has to correct him as five billion, eight hundred million. It is also shown that if someone explains math and calculation too much to him, his head will release steam and eventually explodes like when Knuckle manages to knock him down while explaining about aura calculation.