When Jacob Portman was young he was told by his grandfather that he lived in a special orphanage for children who were peculiar run by a mistress named Miss Peregrine. However, as Jacob grew older he began to question the reality of his grandfather's stories. This changed when Jacob received a distressing phone call from his grandfather, visited his grandfather's home, and found that Jacob was able to see a monster that his friend could not. Abraham, his grandfather, tells Jacob "to find the bird in the loop on the other side of the old man's grave on September 1940" and tell them what happened. Jacob has seen a monster but the police and his parents don't believe the description of the monster, and his parents take him to see a psychiatrist, Dr. Golan. Dr. Golan suggests that Jacob go toWales, the location of the orphanage from his grandfather's stories. Jacob initially finds the orphanage deserted and empty, so Jacob seeks information from the people around that area like the workers at the "Cairnholm museum".
During another search of the orphanage again, he sees a mysterious girl who he follows and tries to get answers from. They reach the bogs before Jacob realizes that the inn and people are different. The people are suspicious about him and an angry mob chases Jacob. Jacob realized he was back in time. Jacob then gets captured by the girl, named Emma Bloom, and an invisible boy named Millard Nillings. The trio drive away the angry mob and escape to Miss Peregrine's orphanage. Jacob is introduced to other children with peculiarities, like his grandfather mentioned. Bronwyn has amazing strength and Claire Densmore who has a mouth at the back of her head. Emma and Millard tell Jacob they are in a time loop that repeats the same day forever because of Miss Peregrine. Miss Peregrine explains to Jacob that she is a Ymbrynes which is a peculiar that can create time loops. Miss Peregrine also explains that a hollowgasts, like the one that killed his grandfather, are a threat to all Ymbryne-run orphanages.
Miss Peregrine explains that Jacob and his grandfather are both peculiar, and their ability is to see and stop the Hollowgasts. Jacob also sees that the peculiar children do performances to entertain the crowd with their powers. Jacob then meets Enoch who has the power to use hearts from other creatures to give life to things for a short time. Jacob and Enoch discover that Victor was killed by a hollowgast and laying dead in his bed. Jacob is told about the wights that have evolved from hollogasts and hunger power from the peculiars. Jacob, Emma, Bronwyn, Enoch and Millard go into an icehouse where a man named Martin who's body was inside an lidless ice coffin so Enoch uses a sheep heart to bring him back to life briefly so Jacob can ask who killed him. Martin explains after realising he's alive that a wight killed him but then the wight turns up behind them and revealed that he is Dr. Golan. Jacob decides that he will stay in the time loop with his friends after all he has been through so he and his companions make their escape from Dr. Golan and make their way back to the orphanage but discover that Miss Peregrine was kidnapped by Dr. Golan.
Dr. Golan said that if they try to rescue her he would kill Miss Peregrine but Jacob and his friend think he is bluffing so they make their way to the shore to find him. When they find Dr Golan near a lighthouse he shoots Millard and they see Miss Peregrine and Miss Avocet in their bird forms in a cage so Jacob and Emma follow him. When they corner Dr. Golan he throws the cage containing Miss Peregrine and Miss Avocet into the water then Jacob shoots him in the throat and he falls into the darkness. Jacob and Emma follow the bird cage to the sea where they see a U-boat and rescue the cage and bring Miss Peregrine back to shore while Miss Avocet is captured by the wights and taken away on the U-boat. Jacob and his companions realise that Miss Peregrine can't change back to human form and when they go back to the orphanage they find it is destroyed which leaves them deciding to track down the wights and figure out how to help Miss Peregrine. Jacob travels back to say goodbye to his father one more time then promises to come back when he has finished his mission with his friends so Jacob and his companions all set sail on a boat to the sea to track down the wights.