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If you check the list of Equestria Girls characters, especially the male students, you possibly might have already glimpsed the human incarnation of Fluttershy's brother.

If Fluttershy has a younger brother, it might be Wiz Kid, Bright Idea, or Micro Chips.

If Fluttershy's bro is an older sibling, Sandalwood and Captain Planet are leading candidates.

UPDATE

One of the students listed as an Equestria Girls character is a male Canterlot High School student named Teddy. Teddy also appeared in an earlier, pre-Friendship is Magic edition of MLP (see mylittleponytales.wikia.com). He also had two male friends named Lancer and Ace. One of this trio of male ponies just might be Fluttershy's brother, and possible the entire trio will make their Friendship is Magic debut in season 6.