Toshiro (Bleach) was able to graduate from the Shinigami Academy in a single year with the highest written and performance scores in each of his classes and to ever reach the rank of captain.
Despite being a high-school student, Prince Akatsuki (Choujin Koukousei-tachi wa Isekai demo Yoyuu de Ikinuku you desu!) is the greatest magician in the world.
Despite being a high-school student, Ichijou Aoi (Choujin Koukousei-tachi wa Isekai demo Yoyuu de Ikinuku you desu!) is the strongest martial art master in the world.
While still a high-school student, Kanzaki Keine (Choujin Koukousei-tachi wa Isekai demo Yoyuu de Ikinuku you desu!) is the finest doctor in the world.
While still a high-school student, Sanada Masato (Choujin Koukousei-tachi wa Isekai demo Yoyuu de Ikinuku you desu!) is the most successful entrepreneur in the world.
While still a high-school student, Ooboshi Ringo (Choujin Koukousei-tachi wa Isekai demo Yoyuu de Ikinuku you desu!) is the most brilliant scientific genius the world has ever known.
Sarutobi Shinobu (Choujin Koukousei-tachi wa Isekai demo Yoyuu de Ikinuku you desu!) a highschool student who is also the world's best journalist.
While still a high-school student, Mikogami Tsukasa (Choujin Koukousei-tachi wa Isekai demo Yoyuu de Ikinuku you desu!) is a genius politician who served as the Prime Minister.
Layfon W. Alseif (Chrome Shelled Regios) is a natural-born prodigy among even the Twelve Heavens Blade, being capable of becoming one at the age of ten. It was stated by even his master Lintence that he could break-down and master Kei Techniques after just seeing them performed once.
Frieza (Dragon Ball series) is a natural prodigy, having been born so powerful that he never had to train a day in his life...
...and when he did decide to train, he gained power comparable to gods within four months.
Rebecca (Dragonar Academy) is the second youngest Breeder to become a Dragonar.
Edward Elric (Fullmetal Alchemist), an alchemical prodigy, became a State Alchemist at age twelve.
Mukuro, later Nobume Imai (Gintama) is a masterful assassin even as a child, her skills earned her the position as one of the Three Wings of Naraku, and often called the "Bastard Child of the Death God".
In addition to his magical aptitude, Negi Springfield's (Mahou Sensei Negima) intelligence is such that he became a homeroom teacher for high school girls at age 10.
Medaka Kurokami (Medaka Box) is a natural genius, progressing through infancy at an accelerated rate and able to surpass even adults in all fields before she was even two years old.
Indra Ōtsutsuki (Naruto) was considered to be a prodigy, which led him to accomplish everything without the need for companions.
Madara Uchiha (Naruto) has been known to be a genius even as a child, being one of the first among the Uchiha to awaken the Mangekyo Sharingan, along with his mastery in fighting.
Sasori (Naruto) was considered as a child prodigy in the art of puppetry, mostly due to his loneliness in lack of parental love motivating his obsession in emotionless puppets.
Itachi Uchiha (Naruto) has been heralded as a genius since childhood, as at age 13 he was selected to be an ANBU captain.
Before leaving the Leaf Village, Sasuke Uchiha (Naruto) was hailed as a genius and was one of the most skilled fighters
of the village.
Himawari Uzumaki (Naruto) not only awakened her byakugan at a younger age then her mom and aunt, but also mastered use of the gentle fist on her very first try.
Tony Tony Chopper (One Piece) had become an outstanding doctor at the age of 15.
Rob Lucci (One Piece) was a prodigy in the Rokushiki martial arts, he could slay 500 soldiers when he was only thirteen years old.
Monkey D. Luffy (One Piece) is the youngest of the Worst Generation, and one of the strongest.
Sabo (One Piece) is one of the most powerful fighters of the Revolutionary army and the youngest.
Minks (One Piece) are natural born warriors from birth.
Charlotte Katakuri (One Piece) is the second strongest member of the Big Mom Pirates, having never lost a single battle since the day he was born.
Charlotte Linlin (One Piece) was born immensely powerful, able to overpower giants even at the age of 5.
Yukari Sendo (Rosario + Vampire) is smart enough to attend high school at age 11.
Erina Nakiri (Shokugeki No Soma) is a child prodigy able to speak at infant stage and gifted with unique ability called "Gods Tongue" making her genius in her academy.