On October 31, 1693, in Salem, Massachusetts, Thackery Binx witnesses his little sister Emily being whisked away to the woods by the Sanderson sisters, three witches who are named Winifred, Sarah, and Mary. Binx confronts the witches, but he fails to save Emily and her life force is drained, making the witches young again. After that, Binx is transformed into a black cat by the witches, cursed to live forever with his guilt for not saving Emily.

Having been alerted by Binx's friend Elijah, the townsfolk arrest the sisters for the murder of Emily. Before the Sanderson sisters are hanged in the town square while they are denying any knowledge of what happened to Thackery, Winifred casts a curse that will resurrect the sisters during a full moon on All Hallows' Eve if a virgin lights the Black Flame Candle in their cottage. Binx decides to guard the cottage so no one can bring the witches back to life.

Three centuries later, on October 31, 1993, Max Dennison reluctantly takes his younger sister Dani out trick-or-treating where they meet Max's new classmate Allison Watts whom he is attracted to. The three visit the former Sanderson cottage, now an abandoned museum, where Max inadvertently resurrects the witches. The witches attempt to suck the soul of Dani, but Max comes to her rescue.

Escaping, Max steals Winifred's spellbook on advice from the immortal cat Binx. He takes the group to an old cemetery where they are protected from the witches since it is hallowed ground. The witches eventually catch up to them at the cemetery where Winifred raises her former love interest Billy Butcherson from the grave and sends him after the children.

The witches pursue the children across town using Mary's enhanced sense of smell. Winifred reveals that the spell that brought them back only works on Halloween and unless they can suck the life out of at least one child, they will turn to dust when the sun rises. After luring them to the high school, the children trap the witches in a pottery kiln and burn them alive. However, whilst the children are celebrating, the witches' curse revives them again.

Not realizing the witches have survived, Max and Allison open the spellbook, hoping to reverse the spell on Binx. The open spell book reveals the location of the group, and the witches track them down, kidnap Dani and Binx, and recover the spellbook. Sarah uses her singing to lure Salem's children to the Sanderson cottage. Max and Allison free Dani and Binx by tricking the witches into believing that sunrise was an hour early. Thinking that they are done for, the witches panic and pass out, allowing Max, Dani, Allison, and Binx to escape.