Léon is an Italian hitman (or "cleaner", as he refers to himself) in the Little Italy neighborhood of New York City working for a mafioso named "Old Tony". One day, Léon meets Mathilda Lando, a lonely twelve-year-old who lives with her dysfunctional family in an apartment down the hall from Léon, and has stopped attending class at her school for troubled girls. Mathilda's abusive father attracts the ire of corrupt DEA agents, who have been paying him to stash cocaine in his apartment. After they discover that he has been stealing the cocaine, DEA agents storm the building, led by their boss, the sharply dressed drug-addict Norman Stansfield. During the raid, Stansfield murders Mathilda's family while she is out shopping for groceries. When she returns, Mathilda realizes what has happened just in time to continue down the hall to Léon's apartment; he hesitantly gives her shelter.
Mathilda quickly discovers that Léon is a hitman. She begs him to take care of her and to teach her his skills, as she wants to avenge the murder of her four-year-old brother. At first, Léon is unsettled by her presence and considers murdering her in her sleep but he eventually trains Mathilda and shows her how to use various weapons. In exchange, she runs his errands, cleans his apartment and teaches him how to read. Mathilda looks up to Léon and quickly develops a crush on him, often telling him she loves him but he does not reciprocate.
When Léon is out on a job, Mathilda fills a bag with guns from Léon's collection and sets out to kill Stansfield. She bluffs her way into the DEA office by posing as a delivery girl, and is ambushed by Stansfield in a bathroom. One of his men arrives and informs him that Léon killed Malky, one of the corrupt DEA agents, in Chinatown that morning. Léon, after discovering her plan in a note left for him, rescues Mathilda, killing two more of Stansfield's men in the process. An enraged Stansfield confronts Tony, who is tortured for Léon's whereabouts.
Léon tells Mathilda about how he became a hitman. When Léon was eighteen in Italy, he fell in love with a girl from a wealthy family, but Léon's family was poor. The two made plans to elope but when the girl's father discovered them, he killed her out of anger. Léon killed the father in revenge and fled to New York, where he met Tony and trained to become a hitman.
Later, while Mathilda returns home from grocery shopping, an NYPD ESU team sent by Stansfield captures her and infiltrates Léon's apartment. Léon ambushes the ESU team and rescues Mathilda. Léon creates a quick escape for Mathilda by smashing a hole in an air shaft. He tells her that he loves her and to meet him at Tony's place in an hour, moments before the ESU team blow up the apartment. In the chaos, a wounded Léon sneaks out of the building disguised as a wounded ESU officer. He goes unnoticed by everyone except Stansfield, who follows him and shoots him in the back. As Léon dies, he presses a grenade pin in Stansfield's palm, saying that it is from Mathilda. Stansfield opens Léon's vest to find a cluster of grenades, which detonate, killing Stansfield.
Mathilda goes to Tony and tries to convince him to hire her, but Tony flatly refuses to hire a twelve-year-old and tells Mathilda that Léon told him to give his money to her if anything happened to him. Tony gives Mathilda $100 as an allowance and sends her back to school, where the headmistress re-admits her after Mathilda reveals what has happened. Mathilda walks onto a field near the school to plant Léon's houseplant, as she had told Léon, to "give it roots".
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