Numbuh Two in Codename: Kids Next Door, he is the one creating and repairing most of the tools and weapons the team uses in their missions.
The titular scientist in Dexter's Laboratory. He is stated to be a small child, yet can build a vast laboratory inside a suburban house, and he can build huge robots and experiments to alter his own body (but cannot keep his sister from disturbing him.)
Teebo from Ewoks is this throughout the first season, though he has moments in the second season as well. He listens to the trees, talks to animals, provides solutions to problems the gang is having and forms a closer bond with Logray, the village shaman.
Ingrid from Fillmore! is the smartest girl in school which is helped by her having a Photographic Memory. She has some nerdy aspects, like owning an Abe Lincoln lunchbox, but it's not played up much.
Jimmy Neutron in The Adventures of Jimmy Neutron: Boy Genius. Who somehow can—among other things—give live to pants, transport himself into dreams, create a time machine, and build a intergalactic messenger out of a toaster.
Gilbert in The Jungle Bunch. One of his favourite pastimes is conducting scientific experiments.
Wade Load of Kim Possible, a ten-year-old super genius who invents all of Kim's gadgets. Oh, and, he's voiced by Taj Mowry, who also played the titular character of a TV show of the Trope Name.
L in Men in Black is the team's scientist, medic and forensic investigator all in one.
Pickles the Drummer, of Metalocalypse, although compared to his bandmates that isn't saying much. Although all of the bandmates have at least one area of expertise despite being catastrophically stupid otherwise, Pickles is implied to be very intelligent: he can play several instruments (and started a highly successful glam rock band as a teenager), understand complex mathematics well enough to explain them to Nathan, read and write music, and seems to have graduated college despite champion-level alcoholism. He might even be a genius, except that because of his implied-to-be-supernatural tolerance, he takes drugs the way other people eat potato chips, and his miserable childhood left him with a level of emotional immaturity that generally puts him on par with the rest of Dethklok.
Twilight Sparkle takes the role in My Little Pony: Friendship Is Magic, though it's subverted more often than not due to her lack of real world experience to back up her vast book learning. She's certainly capable of some Awesomeness by Analysis however, along with some hardcore exposition.
Gretchen Grundler of the Recess gang, she does not make the plans, but is the one checking the numbers to see if they are feasible, and create the gadgets to put it in motion.
Sam Dullard of Rocket Power is a huge computer whiz and uses that knowledge to help the others improve their sports skills every once in a while. He has also skipped a grade.
Velma Dinkley in Scooby-Doo, who is the one that check the clues and actually identifies who the villain is before everyone else.
Kelly Hamdon in SheZow, as she knows everything related to SheZow.
Kyle from South Park often gets this role when compared with the others boys, and even Matt and Trey have called him the group's "smart kid".
Tako, the unofficial leader of the Sushi Pack, is the one usually called on to think of a plan to defeat the bad guys, and even has a standard "thinking routine". He also offers explanations of more complicated terms that come up in the show.
In Teenage Mutant Ninja Turtles (2003), Donatello's intelligence rises sharply to the point where he can build just about anything within a day or two (it seems to vary on how soon the team needs it), and figures out how to adapt Utrom tech, along with almost all other alien technology. He's also the guy with the Simple Staff, and generally considered the Technical Pacifist.
Blossom and Professor Utonium on The Powerpuff Girls both show some moxie in the intelligence department, but they will often get Flanderized (Blossom as egocentric, the Professor as a haplessly overconcerned parent) to keep them from being too one-dimensional.
Egon Spengler in The Real Ghostbusters: All the characters are very intelligent, after all, they are all scientists,note or more exactly: Peter is a social scientist as hes a psychologist, Ray is never specified but is implied that hes a physicist like Egon but his main usage is as The Engineer, Winston does not have any college title but is an expert in mechanics, has military training and is very versatile in non-scientific endevours, so even when not all are officially scientists (unless you count that they all are technically parapsychologists), they all are very intelligent but Egon is so intelligent that he makes the other characters look dumb in comparison. In the Sequel SeriesExtreme Ghostbusters the role lands in Roland.
Sypha Belnades in Castlevania overlapping with The Chick and team mage, shes extremely book smart and figures out how to control Draculas castle. Alucard is almost as smart as Sypha being very well read making a him a Genius Bruiser, both Sypha and Alucard make Trevor Belmont look like Dumb Muscle in comparison despite his leadership skills.
Wildcat in TaleSpin is an exceptionally good mechanic and plane engineer, albeit a little crazy. Some could say that Rebecca is also the Smart Girl of the show as shes the more grounded, but at the same time some of her Get Rich Quick Scheme do not work.
In The Tick, the comics, animated and live-action series, the Tick's moth-garbed sidekick, Arthur, fills the role of the Smart Guy.
In Transformers Generation One, Wheeljack and Ratchet shared this role in the first season, Perceptor joined in as a third Smart Guy in the second season, and the third season saw Perceptor become the sole Smart Guy after Wheeljack and Ratchet's deaths in The Movie. The fourth "season" (really just a few episodes) introduced Brainstorm for this role, but the show ended before much could be done with him.
Winx Club made a half-hearted attempt to avert the "usually the technologically-minded character" aspect by having the girls mention that Musa and Flora get the best grades; nevertheless, the show kept using Tecna in the role of The Smart Girl. Timmy is also one for the Specialists, being the tech expert for them.
In the 4Kids version this turns a little racist; Flora's name is cut out of the best grades line, meaning that Musa, the Asian-inspired character, is the only one mentioned.
Walden from Wow! Wow! Wubbzy! fills this role on the show. As the theme song says, "he knows about science and books and art."
Jingaroo had Humpty Doo, the outback's resident genius who usually has ideas on how to solve problems.
Huey takes on this role in DuckTales (2017) as the smart one of the three brothers, as he's frequently an overachiever, making plans, doing research, and constantly consulting his Junior Woodchuck Guidebook.
Go Go Gophers Ruffled Feather is this, as he often finds out the coyotes' plans and easily comes up with ideas to thwart them. Don't let his unintelligible speech fool you.