Charlie Gordon - The main character of Flowers for Algernon. He is a thirty-two year old man living in New York City who is mentally retarded, and works at Donner's Bakery. He voluntarily goes through an experimental surgery to increase his intelligence. After the surgery, Charlie is constantly battling his emotions, trying to come to an understanding between his feelings and his intellect.

Alice Kinnian
- The woman who teaches Charlie at Beekman's College Center for Retarded Adults. She signs Charlie up for the surgery because of his strong sense of motivation. At first it seems that she is helping Charlie purely for his intellectual growth, but then it becomes more apparent that she is running more on her feelings for Charlie.

Professor Nemur - The scientist in charge of the experiment to increase Charlie's intelligence. Particularly self-obsessed, Nemur treats Charlie like he is a experimental animal and he does not have feelings. He implies that he created Charlie, as if he were referring that Charlie was not human before the surgery.

Dr. Strauss - The neurologist/psychiatrist that performs the operation that raises Charlie’s intelligence. Dr. Strauss also does the therapy sessions for Charlie after the surgery. Unlike Professor Nemur, Dr. Strauss tries to help Charlie overcome his emotional milestones.

Burt Selden - A graduate student who helps Strauss and Nemur in the experiment. Burt watches Charlie and Algernon while they are testing.

Algernon - A white mouse that was the first successful test subject for the intelligence-enhancing experiment. The surgery had made Algernon three times as intelligent as a normal mouse.

Fay Lillman - Charlie’s neighbor in the apartment building that he moves. She is pretty, and free-spirited, and she loves to drink and dance. She and Charlie have a brief sexual affair.

Rose Gordon - A dominating woman who abused Charlie because of his retardation. Even though she was his mother, she did not want to accept that her son was not like other children. She frequently punished him for making a "mess" in his pants, because she could not come to face the fact that her son could have any sign of sexual arousal.

Matt Gordon - A weaker-willed man who dreams of opening his own barbershop. He gave up on Charlie's mother for spending away their savings on "quacks" and protecting Charlie from his mother's bullying wrath.

Norma Gordon - Charlie's sister, who grows up to take care of Charlie's now mentally unstable mother. In her youth, she would be cruel to Charlie because she thought he was getting special treatment. When they meet again, she is happy to see him, and apologizes for her cruelty.

Uncle Herman - Charlie’s uncle, who took care of Charlie after his mother kicked him out. He was very kind to Charlie, and got him a longtime job at Donner's Bakery.

Mr. Donner - The owner of the bakery where Charlie works. A friend of Uncle Herman, Mr. Donner hired Charlie so he didn't have to go to the Warren State Home when Herman died. Donner gave Herman his word that he would look out for Charlie’s interests. Donner stands by his pledge faithfully and treats Charlie like family.

Frank Reilly and Joe Carp - Two employees at Donner’s Bakery who often pick on Charlie. However, Frank and Joe think of themselves as Charlie’s friends and defend him when others pick on him.

Gimpy - A baker at Donner’s Bakery who secretly steals from his boss.

Fanny Birden - The only bakery employee who is always nice to Charlie. When Charlie becomes a genius, Fanny is glad for him, but is very suspicious.

Dr. Guarino - A quack doctor who was kind to Charlie, and promised his mother that he could raise Charlie's intelligence.

Hilda - The nurse on duty while Charlie is first recovering from his operation.

Minnie - A female mouse to keep Algernon company.

Meyer Klaus - A new employee at Donner’s Bakery who is working there before Charlie goes back to his old job because of losing his intelligence.