In 1983, an evil leprechaun (Warwick Davis) is sealed away early in the film by Daniel O'Grady, who had stolen a bag of one hundred gold coins from the little green man, but ultimately paid the price when the Leprechaun scared his wife into falling down a flight of stairs. O'Grady manages to seal the Leprechaun away in his basement by placing a four leaf clover on a crate, which negates the Leprechaun's magic and renders him defenseless. O'Grady attempts to incinerate him, but has a stroke and collapses after screaming "Burn in Hell, you little green bastard!" before he can light a fire. He is later taken to a nursing home, leaving the Leprechaun in the crate.
Ten years later, a man named J.D. Redding (John Sanderford) and his daughter, Tory Redding (Jennifer Aniston) move into the same isolated house, its history unknown to them. Three painters, Nathan Murphy, his eleven-year-old brother, Alex Murphy, and Alex's autistic friend, Ozzie, also accompany them. Ozzie hears the
Leprechaun's cries for help in the basement and unknowingly releases him. The Leprechaun then asks him to tell where the gold is or he'll bite his ear off and make a boot out of it. Ozzie runs away, and attempts to warn the others that there is a leprechaun in the house, but, of course, this falls upon deaf ears.
Later, Alex and Ozzie spot a rainbow above an old truck near the house, which is where O'Grady hid the Leprechaun's gold. Ozzie, biting a coin to determine its authenticity, accidentally swallows it. Alex urges Ozzie to keep quiet about the finding, thinking that he can use the money to fund a brain operation for his friend. The Leprechaun, meanwhile, bites J.D.'s hand while hiding in a tree, though the group was convinced that it was a cat. J.D. is hospitalized; while the rest are with J.D., Alex and Ozzie take one of the coins to a pawn shop owner, who keeps it for further analysis. When the two leave, the Leprechaun sneaks into the store, retrieves his coin, and kills the shop owner by cruelly crushing his chest and stomach while hopping on him with a pogo stick.
On his way back to the house, the Leprechaun is pulled over by Deputy Tribet, which leads him to scratch up the officer's face, throw away his gun, chase him through the woods, and kill him when he snaps his neck. As he arrives at his destination, looking for the bag of gold, he does several odd things, which includes eating a store brand version of Lucky Charms called Lucky Clovers, screaming when he sees himself in a mirror, and polishing the shoes that were in a closet.
Tory, Nathan, Alex, and Ozzie meanwhile return to the home to find it ransacked, and this time, they're convinced that it was a bear. After cleaning up the mess, they hear a sound outside. Nathan goes to check it out, only to get his leg stuck in a beartrap. The Leprechaun tries to "play doctor" by cutting it off with a hatchet, but is shot by Nathan after Alex retrieves a shotgun for him. Ozzie calls the police, only to have them think it was a joke about a killer Leprechaun. They try again, but the line is dead. Later, they try leaving, believing the little man to be dead, but when Alex goes to fix the Distributor Cap, the Leprechaun is hiding under the hood with the cap in his mouth. The Leprechaun bites Ozzie's ear and then gets a lighter stuck in his nose. The Leprechaun then runs back into the barn, makes a little go-cart, and then tips the pickup truck over with the gang still in it. The Leprechaun then chases them back into the house, only to get his hand cut off by a slamming door.
Tory calls the police with her cell phone and gives them the message that someone's trying to kill them, but the Leprechaun tricks the sheriff who calls Deputy Tribet into believing he is the dead officer and tells him to check in on Tory. Ozzie and Alex finally tell Tory and Nathan about the bag of gold and how they hid it in the well. Tory retrieves the bag and gives it to the Leprechaun, but the little man feels he's been tricked since he notices he is missing the gold coin that is in Ozzie's stomach. The Leprechaun tries to kill them, only to get his hand burned by a stove with the tea kettle on and shot twice. He even calls Tory on the house phone and offers "a hand."
Eventually, Tory and Nathan learn that the coin is in Ozzie's stomach and decide that they must kill the Leprechaun without Ozzie having to give himself up. While Tory goes to the nursing home to talk to O'Grady, Nathan and Ozzie distract the creature by throwing shoes for him to shine, which he has no choice but to polish since he is a shoemaker.
At the nursing home, however, Tory finds that O'Grady won't tell her how to kill the Leprechaun. The little green man is in his wheelchair, instead, and chases her into an elevator; O'Grady's mangled body then falls halfway through the ceiling. Just before he dies, he tells Tory that when a leprechaun is in contact with a four leaf clover freshly plucked from the clover patch, it will be as vulnerable as a human.
At the house, after they have found a four leaf clover, the Leprechaun nearly kills Alex, intending to shove his head into a beartrap, leading Ozzie to blurt out that he has swallowed the last gold coin. The Leprechaun, rather than wait for Ozzie's digestive system to produce the coin, instead chases him down and begins slashing his face with his shoe buckle. Alex saves Ozzie by firing the clover, which is wrapped in a piece of gum, at the Leprechaun with his slingshot, catapulting it into his mouth. The Leprechaun's flesh begins corroding rapidly and he falls into the well. As the group rejoins, Ozzie mutters "I did a smart thing, I did a smart thing." Just when they think it is over, though, the nearly-skeletal Leprechaun crawls out of the well, saying, "I want me gold," causing Nathan to hit him with the butt of his gun.
The Leprechaun falls back into the well, and is destroyed when Nathan pours a jug of gasoline into the well and drops a lit match stick into it, causing an explosion.
The police arrive the next morning to find a barely-living Ozzie, Tory, Nathan, and Alex. One officer looks in the well and hears the voice of the Leprechaun, who says: "I'll not rest 'til I have me gold. Curse this well that me soul shall dwell, 'til I find me magic that breaks the spell