There's at least one manga series focused on teaching secondary-level maths. It's a bit dry but gets the job done as an introduction. For something a bit more... specific and involved, there's Cipher Academy, a shonen series where all of the battles take the form of cryptography challenges, often based on esoteric Japanese cultural knowledge (the original English translator dropped the series because it was next to impossible to localize things like "a cipher based on mapping the Japanese syllabary to a list of prefectures").