Convincing arguments can be made either for human-versus-society or human-versus-himself as the novel's central conflict. Ransom Riggs's novel centers on Jacob Portman's quest to help and understand his grandfather, which suggests that the internal conflict is central. Because his grandfather's difficulties were largely caused by the war, however, Jacob struggles to understand how the evil in society could have inflicted such horror on any people—especially children.

Jacob finds himself in the position of challenging the evil in society in order to rescue a few people who are important either in his or in his family's life. He does not intend to take on all of society—or even a large part of it—but his personal convictions ultimately bind him to the struggle against the fascist "Hollowgast."

Jacob tends to romanticize the mysteries in Grandfather Abe's past; he imagines a "magical" explanation for all the fantastic, impossible things he hears about. As he comes to terms with the uniformed, marching "monsters" that actually populate the past, he recognizes the danger of indulging in that kind of romanticism. By facing and overcoming the limitations within himself, he therefore (partly) resolves his internal conflict.

The central conflict of this moving and also hugely enjoyable first time novel by Ransom Riggs is the conflict experienced by Jacob as he tries to come to terms with his life and the murder of his grandfather. As a result, he embarks on a journey, both physical and metaphorical, in which he is forced to learn certain facts about his grandfather's life and the world of which he is a part. This journey is in part a fantastical one, as he realises that the supernatural stories that his grandfather used to tell him were actually true, and he becomes the hero of the day as he is able to protect the "peculiar children" of the title because it is only he who can see the monsters that threaten them. However, above all, the conflict is one of understanding oneself and one's past. Note, for example, the following epiphany that Jacob experiences as he discovers the truth about his grandfather's past, and how the past impacts the present:

I thought about how my great-grandparents had starved to death. I thought about their wasted bodies being fed to incinerators because people they didn’t know hated them. I thought about how the children who lived in this house had been burned up and blown apart because a pilot who didn’t care pushed a button. I thought about how my grandfather’s family had been taken from him and how because of that my dad grew up feeling like he didn’t have a dad. And how I had acute stress and nightmares and was sitting alone in a falling down house and crying hot stupid tears all over my shirt. All because of a seventy year old hurt that had somehow been passed down to me like some poisonous heirloom.

Note here how Jacob is able to see his own problems in the context of the problems experienced by his father and grandfather and great-grandparents. He is able to do this to such an extent that he imagines the "seventy year old hurt" being passed down through the generations like a "poisonous heirloom." However, it is true to say that through understanding one's self, it is possible to understand the world and to gain some measure of meaning in life, and this is certainly how the conflict of this novel is resolved, as Jacob assumes the mantle of hero of the extraordinary children he meets and understands himself at the same time.