May be limited to what field of science they are gifted at.
Depending on the continuity and writers, certain characters may be render useless, overscale, and even be depicted as stupid or idiotic in overall stories or universes.
Senku Ishigami (Dr. Stone) is a scientific prodigy, having knowledge about various fields of science, with a special love of astronomy and space exploration.
Dr. Vegapunk (One Piece) is the leading scientist in the employment of the Marines. His work includes various scientific achievements that are said to be at least 500 years ahead of current technology.
Queen (One Piece) is an extremely talented scientist, inventor, and mechanic who specializes in the creation of biological weaponry, as well as various deadly viruses, and on par with Vegapunk, the world's greatest scientific genius and was his ex-colleague, as well as performing several cybernetic augmentations on his body.
Franky (One Piece) is a genius engineer/shipwright, through self-studying of Dr. Vegapunk's military technology, performed various upgrades on his bionic body with a variety of scientific-based weaponry.
Gretchen Grundler (Recess) is a genius and has the best grades in her school, aside from gym.
Jimmy Neutron (The Adventures of Jimmy Neutron) is nicknamed "Boy Genius" for a good reason
Rick Sanchez (Rick and Morty) was a talented inventor even as a child.
Dr. Henry "Hank" Pym (Marvel Comics)
Reed Richards/Mr. Fantastic (Marvel Comics)
Since a young age, Peter Parker/Spider-Man (Marvel Comics) has been a master scientist with expertise in mechanics, robotics, engineering, and chemistry.
Dexter (Dexter's Laboratory)
Donatello (Teenage Mutant Ninja Turtles)
Miles "Tails" Prower (Sonic the Hedgehog)
Rotor Walrus (Archie Sonic the Hedgehog/Sonic SatAM)
Sento Kiryu (Kamen Rider Build) is described as the smartest Heisei Rider of the Franchise, who in his past identity as Takumi Katsuragi even created the belts that he, Banjo, Gentoku and Kazumi use to transform.
Simon (Alvin and the Chipmunks)
Seto Kaiba (Yu-Gi-Oh) is the inventor of the Duel Disk and Solid Vision.
Orochimaru (Naruto) had a sick fascination with all manner of science and biology. His genius progressed to the point, where he discovered a way to clone himself, transfer his very essence, and etc.