Senku Ishigami (石いし神がみ千せん空くう Ishigami Senkū) is the main protagonist of Dr. Stone, and is friends with Taiju Oki and Yuzuriha Ogawa. He was depetrified half a year before Taiju was, and eventually created the Revival Fluid with Taiju's help.[18] In the Stone World, Senku's goal is to rebuild civilization and establish a Kingdom of Science. 

Taiju Oki (大おお木き大たい樹じゅ Ōki Taiju) is one of the protagonists of Dr. Stone. He was depetrified on October 5th, 5738 AD. Together with Senku, he nobly aspires to rebuild the lost human civilization by depetrifying everyone caught in the phenomenon that happened 3,700 years ago.

Yuzuriha Ogawa (小オ川ガワ杠ユズリハ Ogawa Yuzuriha) is one of Senku's best friends and the love interest of Taiju. Before petrification, she was a high school student and a crafts club member. She was depetrified in 5739 AD. 

Kohaku (コハク) is a young woman who is a descendant of modern humans. She is Ruri's younger sister and the daughter of Kokuyo. She is one of the protagonists of the series. 

Chrome (クロム Kuromu) is the alleged sorcerer and future scientist of Ishigami Village. Originally a rival, he grew close to Senku as the de-petrified human taught him the art of science. He is one of the protagonists of the series. 

Gen Asagiri (あさぎりゲン Asagiri Gen) is a turncoat of the Tsukasa Empire, persuaded to the side of the Kingdom of Science by Senku and the others. He is one of the Five Wise Commanders, specializing in soft skills and interpersonal strategies, but also avoiding hard work if he can help it. When it comes to enemies, Gen acts as a tactical forecaster. Kaseki tends to drag him along to help with crafting, as they are close friends.

Ruri (ルリ) is a descendant of modern-day humans. She is Kohaku's elder sister and the daughter of Kokuyo, and serves as the priestess in Ishigami Village. 

Kaseki (カセキ) is the artisan of Ishigami Village. With expert skill and precision formed by his numerous years of experience as a craftsman[13], he is a key member of the Kingdom of Science, responsible for creating many of their scientific inventions. 

Tsukasa Shishio (獅子王司 Shishiō Tsukasa) is the former primary antagonist of Dr. Stone. He was the antagonist of the first several arcs, his goal being to thin out the human population in order to create a new world without modern technology for the pure-hearted youth. 

Suika (スイカ) is a descendant of modern humans and an inhabitant of Ishigami Village. She is one of the main protagonists of Dr. Stone. Having initially been ostracized for her clumsiness and for wearing a watermelon helmet to compensate for nearsightedness, she quickly makes friends with Senku, who doesn't judge her by her appearance and later helps her regain normal sight through lenses.

 Ginro (銀ギン狼ロー Ginrō) is Kinro's brother, and one of the village guards. He starts hanging around Senku during his stay in the village and is one of the first villagers to join the Kingdom of Science. Being usually used like a "pack mule" for labor in the Kingdom of Science, Ginro tries shirking out of any job he's given regardless of the effort needed; Kohaku and Kinro usually drag him along. During the adventure on Treasure Island, Ginro manages to convince an unpetrified warrior to serve him due to the resemblance he bears to his late master, gaining protection from his former "tormentors".

Kinro (金キン狼ロー Kinrō) is the elder brother of Ginro and the son of Tetsuken and Shirogane. Originally having served as one of the guards of Ishigami Village alongside Ginro[11], he quickly joined Senku as a member of the Kingdom of Science, serving as part of the Power Team's Defense Division. 

Ryusui Nanami (七なな海み 龍りゅう水すい Nanami Ryūsui) is the son of the patriarch of the Nanami Conglomerate and a major player in the Kingdom of Science, along with his devoted butler Francois. He was revived by Senku for his expertise in sailing in order to captain the Perseus to the source of the Petrification. His skills at navigating by sea or air makes him indispensable as one of the Five Wise Commanders. He is also a member of the Crafting and Development Team. 

Hyoga Akatsuki (暁あかつき 氷ひょう月が Akatsuki Hyōga) is a modern time survivor who was revived by Tsukasa Shishio for his excellent spearmanship skills. As an elite member of the Tsukasa Empire, he later betrays Tsukasa but is defeated and jailed by the Kingdom of Science. Currently, he is a member of the Kingdom of Science. 

He is one of the Five Wise Commanders of the Kingdom of Science. He always proposes the use of nonviolence, but will relent if not possible. Because of this, he will push to use Gen's mentalist trickery. Ukyo is in charge of intel gathering and security.