Perfume is the story of Jean-Baptiste Grenouille, a man born into eighteenth-century France with a superhuman sense of smell, but with no personal odor of his own. He is orphaned at birth, and grows up without love to become a cold and calculating murderer. He is motivated in his crime by a desire to possess the scent of a young woman named Laure Richis, which he intends to steal using the extraction methods he has learned as a journeyman perfumer. From this girl's scent, he creates the most powerful perfume in the world, which has the effect of making anyone who smells it fall in love with the wearer. Grenouille uses the perfume to escape punishment for the murders he has committed, even gaining forgiveness from Laure Richis' father. He is not satisfied, however, for he still has no genuine scent of his own. In a bizarre suicidal ending to the novel, Grenouille wanders into a camp of vagrants and douses himself with his powerful scent. In a fit of passion, the vagrants attack and eat him.

Grenouille is born in a fish stall and left among the guts on the ground to die by his mother. She is eventually executed for letting four previous children die, and Grenouille is taken in by the church. The monk in charge of him has trouble finding a wet nurse to feed him, however, because he is a ravenous eater and because he has no smell. He is sent to live with a woman who takes in orphans, Madame Gaillard.

As Grenouille grows up under the harsh but fair hand of Gaillard, he realizes he has an ability that nobody else has, which is a superhuman sense of smell. He is able to detect the slightest odor from across the city, and can use scent the way others use vision to perceive objects. Yet he has no individual scent of his own, something that makes him practically invisible to others, who do not realize that they use their sense of smell to detect the presence of other people.

Madame Gaillard sends Grenouille to work for a tanner named Grimal. He slaves away for years for Grimal, doing the worst of chores, biding his time until an opportunity comes along. He is gradually given more and more freedom by Grimal, which he uses to explore the scents of the city. One night during a fireworks display, he smells a scent so lovely that he is compelled to follow it. It comes from a young woman who is sitting alone in a courtyard. Grenouille comes from behind her and strangles her, taking in her scent as she dies. He creeps away and is not caught.

Opportunity turns up when he is asked to deliver a load of skins to Giuseppe Baldini, a master perfumer. Grenouille maneuvers his way inside Baldini's workshop and talks him into letting him create a perfume for him from the ingredients in his shop. Grenouille has by this time memorized thousands of scents, and has a desire to create new ones by learning the perfumer's art. Baldini is skeptical, but indulges Grenouille.

Grenouille astounds Baldini by creating a perfume that is overwhelmingly beautiful. He takes Grenouille on as an assistant, and exploits his amazing ability to become a rich and famous perfumer. He teaches Grenouille what he can about extracting the scent from natural materials, but Grenouille wants to learn more. Baldini eventually grants Grenouille his journeyman perfumer papers and lets him go, provided he never tell that he was the secret of Baldini's success.

Grenouille sets out for Grasse, the center of the scent-making trade, to learn more about the craft. Once outside the city, however, he begins to avoid the smell of humans, and eventually finds himself on a desolate mountaintop with no trace of human scent. Here he becomes a hermit, living in a dark cave for seven years, during which time he lives in his imagination populated by all the smells he has ever encountered. The most wonderful of these is the scent of the young girl he murdered. Then suddenly he has the realization for the first time that he himself has no smell. He panics and leaves the cave. He decides he must create a scent for himself and makes off toward Grasse. On his way, he is taken in by a nobleman, Taillade-Espinasse, who rehabilitates Grenouille and gives him some money. He steals away from Taillade-Espinasse and makes his way to Grasse.

Arriving in Grasse, Grenouille once again encounters a smell like the one of the girl he murdered in Paris. He follows the scent to the mansion of a scent wholesaler named Richis. It is Richis's daughter that Grenouille can smell, and he begins to devise a plan to possess her scent for himself. He takes a job in a perfumer's workshop and begins to learn more about the methods of extracting scent from things. He begins to experiment with robbing the scent of living beings such as small animals. After some success, he begins to carry out his plan.

The town becomes terrified as several young girls turn up murdered, naked, and with their hair cut off. The killer cannot be found. It is Grenouille killing the girls. He wraps them in oil-soaked linen as they die and extracts their scent. This scent he concentrates into an intense oil he keeps hidden in small bottles in his cabin. The town of Grasse is desperate to stop the killings. One day the killings just stop. After six months, they have largely forgotten about them.

There is one person who has not forgotten the murders, however, and that is Richis. He has decided that he has some insight to the motive of the killer and believes, correctly, that his own daughter is the ultimate target. He packs up his household and pretends to leave for the town of Grenoble. On the way, he and his daughter break away and head toward the sea. He intends to have her married to the son of a baron right away. Once she has lost her virginity, he reasons, the killer will no longer desire her.

Grenouille is able to track them with his nose, however. While they are stopped at an inn, he climbs into Laure's window and kills her, taking her scent as he has done with the other girls. He gets away and returns to Grasse.

He is soon caught, as he had been seen at the inn. He confesses to the murders and is sentenced to be executed. On the day of the executions, however, he steps out of the carriage that is carrying him to the scaffold, wearing the ultimate perfume that he has created from the scents of his murder victims. At once the crowd is convinced that he must be innocent. The scent makes them feel they are in love with him, and that he must be set free. Even Richis falls into tears, begging Grenouille to forgive him. Meanwhile, the amassed crowd descend into a gigantic sexual orgy.

Grenouille passes out. He is overcome once again by the panic that he has no scent of his own. He wakes up in Richis's mansion, in Laure's very bed. Richis asks him to be his adopted son, he loves him so much. Grenouille agrees, but as soon as possible he leaves the mansion and sets of out of Grasse toward Paris, with a bottle of his ultimate perfume.

He is going to Paris to die. He can make people love him with his perfume, but it will only ever be a hollow love because he has no scent of his own. He enters Paris and goes back to the neighborhood where he was born, near a foul-smelling cemetery. There, a group of vagrants have built a small fire and are gathered around it. Grenouille steps into the circle of vagrants and douses himself with the ultimate perfume. The vagrants are overcome with love and desire for Grenouille, to the point that they attack and eat him.