This seems pretty straightforward, right? The Boy in the Striped Pajamas is a description of what Bruno sees on the other side of the fence:
He wore the same striped pajamas that all the other people on that side of the fence wore and a striped cloth cap on his head. (10.535)
We're at the midway point in the novel here, and introduced to Shmuel, Bruno's friend on the other side. But there's a catch: Shmuel isn't the only boy who wears striped pajamas, and no, we're not talking about his fellow prisoners. We dig into this big time over in the "Symbols" section, so be sure to check it out, but right now we'll leave you with this: Bruno puts them on, too. And when he does, we're pretty sure he's the boy in striped pajamas the title refers to.
But seriously—hop over to the "Symbols" section pronto. You won't be sorry… though you may never look at jammies the same way again.