Florida teenager Jake Portman (Asa Butterfield) feels trapped in a monotonous life until a disturbing call from his grandfather, Abe (Terence Stamp), propels him into a whirlwind of mystery and danger. Concerned about Abe's fearful demeanor, Jake rushes to his grandfather’s home with his supervisor, Shelley (O-Lan Jones), where they encounter a sinister man with eerie white eyes (Samuel L. Jackson). Inside, Jake is horrified to discover the house in disarray and Abe lifeless, stripped of his eyes after issuing a grim warning. Moments after Abe’s death, a terrifying creature approaches, but Shelley, armed and ready, sees nothing, leaving Jake consumed by questions.
In search of clarity, Jake visits his psychologist, Dr. Golan (Allison Janney), expressing his belief that Abe's death has a deeper connection than a simple heart attack. Memories resurface of his youth, where Abe enthralled him with fantastical tales of children with extraordinary abilities, overseen by a mysterious woman named Miss Peregrine (Eva Green). Upon receiving a book from Abe containing a postcard from Miss Peregrine inviting him to her home, Jake is determined to seek answers, prompting a reluctant agreement from his parents to let him travel to the enchanted island of Cairnholm in Wales.
Accompanied by his father, Franklin (Chris O'Dowd), Jake embarks on the journey, spotting a peregrine falcon—a symbol he connects to his adventures with Miss Peregrine. However, upon arrival, he is disheartened to find the home in ruins, leading him to believe that Miss Peregrine and her peculiar children might have perished. Yet, he stumbles upon a group of strange children, only to panic and black out.
When he awakens, he finds himself in the protective grasp of Bronwyn (Pixie Davies), a girl with remarkable strength. As he meets the peculiar kids, each possessing unique powers—like Emma (Ella Purnell), who can control air at the cost of lead shoes; Olive (Lauren McCrostie), who wields fire; and Hugh (Milo Parker), harboring bees inside him—Jake learns the truth of their existence in a time loop that preserves them from the perils of the outside world.
Under the guidance of Miss Peregrine, Jake also learns about their enemy, Mr. Barron, and the terrifying Hollowgasts—monsters that prey on Peculiars. Over dinner, Miss Peregrine explains their precarious situation, living eternally on September 3, 1943, just a day before a bomb threatens their lives. As Jake bonds with the children, he witnesses their extraordinary abilities, including prophetic dreams and brief resurrections.
Tension builds as Jake receives a warning about Barron, whose motive to hunt the children becomes clearer. As they navigate treacherous encounters, the children devise a plan to prevent the dark forces from claiming their lives. With thrilling action sequences, they summon their powers, throwing cotton candy and resurrecting skeletal puppets to fend off Barron and his Hollow cronies, culminating in an intense battle that tests their courage and bonds.
Finally returning to his own time, Jake must reconcile the adventure with the price of his newfound friendships. In a heartwarming reunion with Abe, Jake shares tales of the extraordinary world he visited. With one final leap of courage, he races to meet Emma as they embark on a new adventure together, signifying that while they may be separated by time and space, the magic of their bond will endure.
