Charlie Gordon, the novel's narrator, is an intellectually disabled man who yearns to be smarter. When he was young, his mother was tormented about his disability and wanted only for him to be "normal." She was abusive toward him, and Charlie's father failed to protect him from her abuse. When Charlie's sister was born without a disability, his mother rejected Charlie and sent him away. As an adult Charlie learns to read and write to some extent at the Beekman College Center for Retarded Adults, and works at a bakery where the other workers make fun of him and mistreat him. He agrees to undergo an experimental treatment previously performed only on a mouse, Algernon. After Charlie's brain is surgically altered, he, like Algernon, becomes increasingly and brilliantly intelligent. He then finds an error in the experiment that reverses all and will lead to a loss of intelligence and death. Charlie gradually loses all he had gained.
Algernon is a white laboratory mouse who has had brain surgery to increase his intelligence. The experimental surgery is a success, as evidenced by Algernon's ability to run through a maze at speeds much greater than a regular mouse. However, Algernon sometimes refuses to run the maze and throws himself at its walls. Charlie grows fond of Algernon and takes him to live in his apartment, where Algernon is soon joined by a female mouse companion. Algernon's behavior becomes erratic and violent as his intelligence declines, and finally he dies.
Professor Harold Nemur is an egotistical psychology professor at the Beekman College Center for Retarded Adults. Along with Dr. Strauss, he designs and directs the project to increase human intelligence. He sees Charlie and Algernon as tools to help him succeed in his experiment and burnish his reputation. Nemur starts to treat Charlie as a person only after Charlie's intelligence increases, though he still shows little concern for him; he later feels threatened by Charlie's intelligence when it surpasses his own.
Dr. Strauss is a psychiatrist and a neurosurgeon working at the Beekman College Center for Retarded Adults. Along with Professor Nemur, he designed the project to increase human intelligence, and he psychoanalyzes Charlie and reads his progress reports. Somewhat more caring toward Charlie than the older Professor Nemur, Strauss is still motivated largely by ego.
Rose Gordon, Charlie's mother, at first denies he has an intellectual disability, insisting he is like other children. She is often physically abusive when he does not meet her expectations and demands. When Charlie is a young boy, she takes him to a dishonest doctor who claims he can make Charlie smarter, and she refuses to have Charlie admitted to the Warren State Home, an institution for the mentally disabled. After Rose has a daughter, Norma, who has no disabilities, Rose withdraws from Charlie and begins worrying he is a threat to Norma and will ruin their social standing. She punishes him for showing signs of sexual development and then rejects him from the house to protect Norma. In her old age she becomes senile; when she briefly recognizes Charlie, she tells him his increased intelligence was an answer to her prayers.
Alice Kinnian, known to preoperative Charlie as Miss Kinnian and to postoperative Charlie as Alice, is a teacher at the Beekman College Center for Retarded Adults. She takes special notice of Charlie because of his good nature and motivation to learn, and recommends him as a candidate for the experimental treatment. She becomes attracted to Charlie as his intelligence increases, but she worries about becoming involved with him because he is changing so rapidly. When he becomes smarter than she is, she doubts herself and distances herself from him. As his intelligence starts to decline, she moves in with him, and they have a loving sexual relationship. However, as his intelligence continues to decline, he becomes irritable and depressed and asks Alice to move out. He says goodbye to her in his final report.