The theme of Miss Peregrine's Home for Peculiar Children is the power of family and friendship.

The protagonist, Jacob Portman, has a close relationship with his grandfather, Abraham, but once Jacob grows older he also grows a bit distant from Abraham. He still loves and admires his grandfather, however, despite all of Abraham's flaws, and is deeply saddened by Abraham's death. Jacob also has an complicated relationship with his parents, as he struggles to get along with them. His father, Franklin, and his grandfather have a difficult relationship as well, as Abraham neglected his son, and Franklin felt that his father simply didn't love him enough.

Jacob discovers that the stories his grandfather told him about a strange home for special and magical kids weren't actually fairy tales. Thus, Jacob goes on an adventure to find Miss Peregrine and her Home for Peculiar Children, hoping to uncover the mystery of his grandfather's childhood and to uncover who he truly is. About his grandfather, Jacob says,

I guess he'd seen it coming—I had to grow out of [his stories] eventually—but he dropped the whole thing so quickly it left me feeling like I'd been lied to. I couldn't understand why he'd made up all that stuff, tricked me into believing that extraordinary things were possible when they weren't. It wasn't until a few years later that my dad explained it to me: Grandpa had told him some of the same stories when he was a kid, and they weren't lies, exactly, but exaggerated versions of the truth—because the story of Grandpa Portman's childhood wasn't a fairy tale at all. It was a horror story.

At Miss Peregrine's home, Jacob makes a deep and special connection with all of the peculiar children, who become his friends. Thus, he learns that family doesn't always mean that you have to be related by blood; family and home are where the heart is. At the same time, he comes to a new understanding of his father, his grandfather, and himself, which further strengthens the theme of family.