Washu from Tenchi. Though to tell the truth, the way she zipped around like a clown through the series didn't show off her legendary intelligence, still her background is compelling :P
No scientists in history not Sir Isaac Newton, not Albert Einstein not Stephen Hawking, not Galileo Galilei, not Leonardo Da Vinci nor Giordano Bruno or Carl Sagan would be able to share a stage with this pink-haired lady without being laughed off of it, her inventions would leave everyone in the dust!
While with such fierce competition she may not win the day, still I think Edward Wong Hau Pepelu Tivrusky the 4th also deserves an honorable mention at least. Maybe she could win a "youth prize" for academic excellence? Or be the winner of the international anime chess contest?