Plot
During a visit to his grandmother Helga in Norway, an eight-year-old American boy Luke Eveshim is told about "witches", feminine demons who detest children and use various methods to dispose of them while masquerading as ordinary women. They are described to have claws instead of fingernails which they hide by wearing gloves, bald heads which they obscure with wigs that give them rashes, square-ended and toeless feet that are concealed by sensible shoes, a purple tinge in their pupils and a powerful sense of smell which they use to detect children. To a witch, clean children are repulsive; the dirtier the children, the less likely they are to smell them. Helga additionally recounts how her childhood friend, Erica, fell victim to a witch who lived opposite to her and was cursed to spend the rest of her life trapped inside a painting, aging gradually and changing her position within it, until finally disappearing a few years prior.
After Luke's parents die in a car accident, Helga becomes Luke's legal guardian and they move to England. While playing outside, Luke is approached by a woman he identifies as a witch, trying to lure him to her with a snake and a chocolate bar, so he stands his ground and the witch leaves. He had already heard one of his friends mention that he had recently seen a woman with purple eyes.
On Luke's ninth birthday, Helga contracts diabetes; her doctor advises them to take a holiday at a hotel by the English seaside. There, Luke meets and befriends gluttonous but friendly Bruno Jenkins, while unintentionally antagonizing the hotel manager, Mr Stringer, after his pet mice frighten his maid girlfriend. Also staying at the hotel is a convention of witches, masquerading as the Royal Society for the Prevention of Cruelty to Children (RSPCC). The Grand High Witch, the all-powerful leader of the world's witches, is attending under the alias Eva Ernst.
As Luke hides and spies on the witches' meeting, the Grand High Witch unveils her latest creation – a magic potion to transform all the world's children into mice, which will be used in products at confectionery stores to be purchased using money she provides. Bruno, who was given the potion earlier, is lured into the room, transforms into a mouse and flees. Luke is discovered and, after a chase, runs to Helga in their room but finds her in a diabetes-induced state. He is then captured by the witches as they force-feed him the potion, transforming into a mouse before he escapes. He finds Bruno and reunites with Helga, who has since recovered. Luke, now a mouse, devises a plan to defeat the witches by sneaking into the Grand High Witch's room to steal a bottle of the potion and putting it into the cress soup for an upcoming banquet. The Eveshims try to get Bruno to his parents, but they do not believe them and are frightened by his condition.
Luke narrowly manages to obtain the formula and sneaks into the kitchen where he puts it into the soup. As the witches attend the banquet, Susan Irvine, the Grand High Witch's much-abused assistant, quits upon being banned from the celebration. At dinner, Bruno's father orders the soup, though Helga stops him from consuming it as Mr and Mrs Jenkins finally realise what the witches did to their son when he speaks up. The formula then turns all the witches into mice and the hotel's staff and guests join in exterminating them, unknowingly ridding England of its witches except Irvine, who shows up later completely shocked at the sight.
Helga traps the Grand High Witch under a water jug and leaves Stringer to dispatch her with a cleaver before returning Bruno to his bewildered parents. The Eveshims return home and receive a delivery of the Grand High Witch's trunk full of money and an address book of all witches in the United States, allowing them to plan their move against these witches.
That night, a now-reformed Irvine visits the Eveshims' house and returns Luke to his human form, as well as his returning his pet mice and glasses, before leaving to do the same with Bruno as the Eveshims bid her farewell.