Jacob Portman believes he is ordinary and is fascinated with his extraordinary grandfather, Abraham Portman, during his childhood years. Grandpa Portman introduces Jacob to interesting stories about monsters and unusual pictures of peculiar children. As a child, Abraham escaped Nazi Germany to Wales, where he lived in a house with other children under the guidance of Headmistress Peregrine.

The older Jacob becomes, however, the more disbelief he has toward his grandfather’s stories. Similarly, Jacob’s family thinks his grandfather is crazy, particularly as he ages and begins to insist that monsters are after him. One day, Jacob is interrupted at work with a call from his grandfather, who is looking for the key to his gun trunk. Abraham tells Jacob that the monsters are coming to get him and that he needs to protect himself. Thinking his grandfather is simply being melodramatic, Jacob goes to his grandfather’s, where he finds the house a mess and his grandfather dying.

That night, among the Palmetto trees, Jacob sees a tentacle-mouthed monster, which sends him reeling into confusion: were his grandfather’s stories of monsters true? Abraham’s dying words further confuse Jacob: Abraham gives him clues and asks him to find a loop and a bird on the other side of an old man’s grave. Jacob does not understand what his grandfather means. After the incident, Jacob’s family worries about him and sends him to a psychiatrist named Dr. Golan.

Dr. Golan convinces Jacob he has post-traumatic stress disorder, and Jacob withdraws into isolation. On his sixteenth birthday, Jacob’s aunt gives him the gift that ultimately changes his life: a collection of Emerson’s works that contains a letter from Miss Peregrine to his grandfather. Dr. Golan gives his permission for Jacob to travel to Wales, and Jacob’s father, Franklin, accompanies him to an island named Cairnholm.

Once on Cairnholm, Jacob dives into his grandfather’s story and searches for the children’s’ home his grandfather once inhabited. He expects to find it intact and inhabited, however, much to his surprise, the house is in shambles, the result of a bomb around the time his grandfather lived in the house. Unsure whether he wants to continue to delve into the story, Jacob almost gives up on understanding his grandfather. His father’s own story about how he used to be interested in Abraham’s life but suspected there was another woman and another family, motivates Jacob to continue on.

One day at the wrecked house, the silence is interrupted by a girl’s voice calling out for “Abe.” Jacob finds himself chasing children through the bogs on the island, until he finds a cairn, the final resting place of a 16-year-old boy from long ago, which is now showcased in the island’s museum. He enters the cairn and reemerges in a different time: 1940. Diesel engines no longer grace the streets, and carts are moved by horses. Jacob is captured by the children and brought before Miss Peregrine. The children’s home is intact, and there is no evidence of a bomb ever having hit it. Miss Peregrine knows Jacob is Abraham’s grandson and welcomes him to their home. She explains the cairn leads to a loop, a place stuck in time, which she maintains. He learns that each child is peculiar and has a power: some can use fire, some have incredible strength, and some have prophetic dreams.

Jacob finds himself lying to his father about where he goes each day, telling him he has met people on the other side of the island. The more time he spends in the loop, the more he gets to know Emma, who was once his grandfather’s sweetheart. They form a bond, and soon Jacob begins to question whether he should stay in this world or if he should go. Questions arise when another peculiar child tells Jacob to check out a room at the end of the hall in the house. Inside lies a dead boy.

Jacob questions how the boy died, and Emma promises to tell him one night. He meets her, and they go to a shipwreck where Jacob’s life changes for good. Emma tells him that he is just like his grandfather and that his grandfather had the power to see monsters. Jacob has the same power.

After he finds out about his power, danger approaches. A new man comes to the island, and then Miss Avocet, another bender of time who can create loops, shows up and tells Miss Peregrine that hollowgast are tracking down and killing peculiars. Soon, a man goes missing on the island and turns up dead. Jacob and the children go to find out what happened and are accosted by Dr. Golan and the tentacle mouthed monster. They are working together to capture all the women like Miss Peregrine. Dr. Golan leaves them to die at the tentacle monster’s hands.

They escape and track down Dr. Golan, who has taken Miss Peregrine and Miss Avocet. After working together, Jacob and the other peculiar children defeat Dr. Golan and save Miss Peregrine, who is trapped as a bird. To save the other peculiars in other loops, the children decide to leave together and search the loops to stop the hollowgast.