There are so many Prodigies in Naruto series. I made a list of child prodigies from naruto. This list is not in order and based on my personal opinion.
1. Itachi Uchiha
The 3rd hokage said Itachi was already thinking like a Hokage when he was 5 years old. At the age of 7 Itachi awoke his sharigan and mastered it in a year so by age 8 he had the full 3 tomoe. Then he was 13 when he gained the Mangekyo from Shisui’s death. At the age of 11 he entered the Anbu. . By age 13, he was promoted to Anbu captain.
The sole survivor of the Yuki clan, and the subordinate of Zabuza. Haku, despite being young, holds enough potential and strength to surpass any ninja. Using his ice based bloodline and intelligence.
3. Neji Hyuga
Neji was a born in the Hyuga Branch family. He had mastered almost every high level techniques of the Hyūga Clan and byakugan
4. Madara Uchiha
Madara was born in the Uchiha clan. He awakened Sharingan at very young age and later mastered Mangekyo Sharingun too. He become leader of Uchiha clan during his youth. He is the strongest and most feared Uchiha in the history of hidden leaf village
5. Minato Namikaze
Minato graduated from academy at very young age. He also holds the record of highest score in the history of the academy. His potential was acknowledge by Jiraiya. He was the 4th Hokage.
Orochimaru is one of Konohagakure’s legendary Sannin. He was trained by the 3rd hokage- Hiruzen. Orochimaru stood out as a genius — his talents, knowledge, and determination were considered to be that of a prodigy seen only once in a generation.
Sasori mastered the art of puppetry during his childhood. His skills improved with time and he created many puppets including Kuroari,Karasu, and Sanshōuo.Sasori secretly kidnapped theThird Kazekageand made him into one of his human puppets. He became a member of the Akatsuki and teamed up with Deidara