Algernon
Algernon is the mouse that was the initial subject of the surgery which enhanced Charlie's intelligence. Charlie develops a close emotional connection with Algernon, who is the only other being to have its intelligence artificially increased. Algernon's experiences and fate closely mirror Charlie's own journey.

Fanny Birden
Fanny Birden is an older woman working at the bakery with Charlie and is the only employee who refuses to sign a petition demanding Charlie's resignation after his IQ improves. She likens the change in Charlie's intelligence to Adam and Eve eating from the Tree of Knowledge and wishes Charlie "could go back to being the good simple man you was before."

Joe Carp
Joe Carp is one of Charlie's colleagues at the bakery and, along with Frank Reilly, is one of his main tormentors.

Mr. Arthur Donner
Mr. Donner, the owner of the bakery where Charlie works, is a friend of Charlie's Uncle Herman and gave Charlie his job. Unlike many others at the bakery, he treats Charlie kindly, albeit somewhat condescendingly.

Gimpy
Gimpy is a worker at Donner's bakery who treats Charlie better than many of the other employees. However, Gimpy becomes the cause of one of post-operative Charlie's first significant crises when Charlie catches him stealing from the cash register. When confronted, Gimpy says, "I always stood up for you. I should of had my head examined."

Charlie Gordon
Charlie Gordon, the narrator and main character of Flowers for Algernon, is a 32-year-old man with an IQ of 68. As a child, Charlie had a father who loved and tried to care for him, but he was subjected to abuse by his emotionally unstable mother. Initially, his mother refused to acknowledge that anything was "wrong" with Charlie and would beat him when he failed to meet the standards of other children. After the birth of Charlie's sister, who had normal intelligence, his mother admitted his disability but became obsessed with the fear that Charlie would harm his sister, particularly that he might sexually molest her. This irrational fear led her to violently suppress any display of sexuality on Charlie's part and eventually to threaten to kill him if he was not removed from their home.

This pattern of childhood abuse left a significant impact on adult Charlie, manifesting in repressed sexuality and a strong desire to learn. It was this latter trait that led him to attend night classes at the Beekman School and ultimately to be selected for an operation to boost his intelligence. Before the operation, Charlie is seen as a "good, simple man" and a "likeable, retarded young man." His primary goal in undergoing the operation is "to be smart like other pepul so I can have lots of friends who like me."

Once Charlie achieves normal intelligence, he realizes that many individuals he considered friends were actually mocking and mistreating him. Upon reaching a genius-level IQ, he finds himself just as isolated and alienated from others as before. He grapples with emotions he now understands intellectually but cannot manage solely through intellect. Additionally, he strives to reconcile and come to terms with memories from his childhood. Throughout all these changes, Charlie's primary desire remains unchanged: to be treated as a human being and to form meaningful relationships with others.

Despite displaying some character flaws, such as arrogance and self-absorption, after his intelligence peaks, Charlie fundamentally remains a good person. When he discovers that the surgical procedure is flawed, he dedicates himself to research in hopes of identifying the issue. He believes that if his efforts can contribute to "the possibility of helping others like myself, I will be satisfied." Upon concluding that nothing can prevent his regression to his pre-operative state, he attempts to reconcile with his family and those around him. In turn, they come to recognize his value as a person. Even when Charlie reverts to his previous subnormal intelligence, he has learned to be empathetic towards others' shortcomings, understanding that they are "not so smart like you once thot they were." Though the experiment fails, Charlie Gordon does not.

Matt Gordon
Charlie's father, a salesman of barbershop supplies, is fundamentally a kind man who loves his son and seeks to protect him. However, he is often overwhelmed by his wife: first, by her hysterical denial of Charlie's handicap, and later by her equally hysterical belief that Charlie poses a threat to their daughter. When Rose threatens to kill Charlie, Matt takes him to his Uncle Herman, who provides Charlie with a safe haven. Years later, Matt separates from Rose and opens his own barbershop. When the adult Charlie seeks him out, Matt does not recognize his son.

Norma Gordon
Norma Gordon is Charlie's sister. Charlie remembers her as a "spoiled brat" who mistreated him and harbored animosity towards him. However, when the adult Charlie visits the adult Norma, who now cares for their senile mother full-time, he discovers a woman who is "warm and sympathetic and affectionate." She sincerely regrets her past hostility towards her brother and wishes to reconnect with him.

Rose Gordon
Charlie's mother, Rose Gordon, is an emotionally unstable woman who struggled to cope with having a mentally handicapped child. During Charlie's early years, she refused to acknowledge his condition and punished him for not performing at the same level as other children. After the birth of Charlie's sister, Norma, who did not have any mental handicaps, Rose stopped trying to make Charlie "normal" and became fixated on "protecting" Norma from him. Eventually, Rose had a complete breakdown, claiming Norma was in danger of being sexually molested by Charlie and threatening to kill him if he wasn't removed from their home. When Charlie reconnects with his mother many years later, he finds an elderly woman deep into senility who barely recognizes him.

Hilda
Hilda is a nurse who cares for Charlie immediately after his operation. She tells him that the scientists should not have altered his intelligence, comparing their actions to Adam and Eve eating the fruit from the Tree of Knowledge and being cast out of Eden.

Miss Alice Kinnian
Miss Alice Kinnian is Charlie Gordon's teacher at the Beekman University Center for Retarded Adults. She is the one who recommends Charlie for the procedure that enhances his intelligence and the woman he loves. Alice is an intelligent and dedicated teacher who takes a deep personal interest in Charlie and always treats him responsibly and respectfully. As Charlie's intelligence grows, she guides him as best she can. When he falls in love with her, she gently declines his advances. Despite this, they maintain a close friendship, and Alice eventually reciprocates Charlie's feelings, only to find that his past traumas prevent him from being intimate with her. She remains his friend despite the growing intellectual gap between them. When the operation ultimately fails and Charlie's intelligence declines, they finally establish a romantic relationship. Alice tries to support Charlie, even when he pushes her away, but when he regresses to his original IQ of 68, she has to accept that he is lost to her and move on with her life.

Fay Lillman
Fay Lillman is a free-spirited artist living across the hall from Charlie when he "disappears" in New York. When Charlie first sees her painting in her underwear, she is unfazed and doesn't hesitate to crawl along a window ledge to reach Charlie's apartment. Eventually, Charlie enters a sexual relationship with her, despite not loving her. Fay brings Charlie into a whirlwind lifestyle filled with social events, drinking, and dancing. Although she seems to care for Charlie, she shows no interest in his research, possibly because she is unaware that Charlie's intelligence has been artificially enhanced. When Charlie moves into the lab because Fay disrupts his work, she loses interest in him and drifts away.

Bertha Nemur
Bertha Nemur, the wife of Professor Harold Nemur, is an ambitious woman who used her father's influence to secure the grant funding her husband's research. She constantly pressures him to excel and achieve significant results. Burt Selden notes that she is the reason Nemur is "under tension all the time, even when things are going well…."

Professor Harold Nemur
Professor Harold Nemur, the psychologist behind the theories of the operation that increased Charlie's intelligence, is a brilliant yet egotistical and ambitious scientist. His ambition is partly driven by pressures from his wife. Desperate to establish his reputation as the discoverer of the process that made Charlie a genius, he rushes to publicize the experiment's results, ignoring the advice of other scientists involved. Initially, he is reluctant to use Charlie as the subject of the experiment. After Charlie's IQ increases, their relationship becomes strained, as Charlie's intelligence eventually surpasses Nemur's. This tension culminates in a heated argument where Charlie accuses Nemur of dehumanizing him, and Nemur retorts that Charlie has become "arrogant, self-centered," and "antisocial."

Frank Reilly
Frank Reilly is one of Charlie's coworkers at the bakery and, along with Joe Carp, one of his main tormentors.

Burt Seldon
Burt Seldon is a graduate student assisting Professor Nemur and Dr. Strauss. He oversees Charlie's psychological testing and treats him more amicably and informally than the senior scientists. Burt provides Charlie with much of his information about Nemur and Strauss and suggests that the post-operative Charlie needs to develop "understanding" and "tolerance."

Dr. Strauss
Dr. Strauss, Professor Nemur's partner, is the neurosurgeon who performs the surgery that enhances Charlie's IQ. He is more compassionate and concerned for Charlie than Nemur. Strauss advocates for Charlie to be selected for the experiment, intervenes during a potentially violent confrontation between Charlie and Nemur, and tries to care for Charlie when the effects of the experiment begin to fade.

Thelma
Thelma works as a nurse at the Warren State Home and earns Charlie's admiration through her dedication to her patients. Aware that he is deteriorating and may eventually become a resident at Warren, Charlie contemplates what it would be like to have her look after him.

The protagonist and main character of Flowers for Algernon, Charlie Gordon, is a 32-year-old man with an IQ of 68. In his childhood, Charlie had a loving father who tried to care for him, but he suffered abuse from his emotionally unstable mother. Initially, his mother refused to acknowledge that there was anything "wrong" with Charlie and punished him when he failed to meet the standards of other children. When Charlie's sister was born with normal intelligence, his mother finally admitted his disability but became obsessed with the fear that Charlie might harm his sister, particularly through sexual molestation. This irrational fear led her to violently suppress any expression of sexuality from Charlie and ultimately to threaten to kill him if he wasn't removed from their home.

This traumatic upbringing left a lasting impact on Charlie, particularly in two areas: repressed sexuality and a strong desire to learn. His determination to learn led him to attend night classes at the Beekman School, which resulted in him being selected for an operation to increase his intelligence. Prior to the surgery, Charlie was seen as a "good, simple man" and a "likeable, retarded young man." His primary motivation for undergoing the procedure was "to be smart like other pepul so I can have lots of friends who like me."

However, after achieving normal intelligence, Charlie realizes that many of the people he considered friends were actually mocking and mistreating him. Upon reaching a genius-level IQ, he feels just as isolated and alienated as before. He struggles to manage the emotions he now understands but cannot fully control with intellect alone. Additionally, Charlie works to confront and reconcile with memories of his childhood. Throughout his journey, Charlie's central desire remains the same: to be treated as a human being and to form meaningful relationships with others.

Despite exhibiting some negative traits after his intelligence peaks, such as arrogance and self-centeredness, Charlie remains fundamentally a good person. When he discovers the flaw in the surgical procedure, he dedicates himself to research in an effort to help others, stating that if his work can contribute to "the possibility of helping others like myself, I will be satisfied." When he ultimately concludes that nothing can prevent his regression to his pre-operative state, he seeks to make peace with his family and those around him, and they come to recognize his value as a human being. Even after Charlie returns to his previous level of intelligence, he has learned to be understanding of others' shortcomings because they are "not so smart like you once thot they were." Although the experiment fails, Charlie Gordon himself does not.

Flowers for Algernon tells the story of a mentally impaired man who undergoes surgery to enhance his intelligence, only to eventually lose it again. This narrative explores several literary themes, with the most prominent being the use and misuse of science and technology. Critic Mark R. Hillegas categorizes Flowers for Algernon as a type of science fiction that addresses "problems imagined as resulting from inventions, discoveries, or scientific hypotheses." In this case, the story revolves around a surgical procedure that transforms a person with below-average intelligence into a genius. Although the novel does not explicitly criticize technology, it highlights its limitations as a "quick fix" for human issues—Charlie's operation ultimately fails because he does not remain a genius. Contrary to the traditional concept of tragedy, Charlie's downfall is not due to a personal flaw but rather the flawed technology intended to change him.

The notion that "there are some things humanity was not meant to know" can be traced back to Mary Shelley's Frankenstein (1818), and in many ways, Flowers for Algernon echoes Shelley's story. Critic Thomas D. Clareson has directly linked Keyes's novel to Frankenstein, noting that Keyes merges the roles of the mad scientist and the "inhuman" creation into "the single figure of Charlie Gordon." This theme is further underscored by the remarks of Hilda, a nurse, and Fanny Birden, one of Charlie's coworkers. Both characters liken his operation to the acquisition of forbidden knowledge in the Garden of Eden, which led to Adam and Eve's expulsion from Paradise.

However, Flowers for Algernon does not suggest that we should avoid seeking knowledge. Instead, it advises awareness of the limitations of a solely intellectual life. When Charlie immerses himself in research to fix the flaw in the operation, he states, "I'm living at a peak of clarity and beauty I never knew existed." Later, during an argument with Professor Nemur, Charlie admits that intelligence alone is insufficient: "intelligence and education isn't worth a damn... all too often a search for knowledge drives out the search for love."
In an early "progress report," Charlie expresses his desire to be smart "so I can have lots of friends who like me." Unfortunately, after becoming a genius, he encounters a new set of problems that hinder his ability to form meaningful relationships. He experiences a different kind of alienation, where the condescension and cruelty he once faced are replaced by misunderstanding, insensitivity, and fear. Charlie falls in love with Alice Kinnian, the teacher who recommended him for the operation, but realizes, "I am just as far away from Alice with an I.Q. of 185 as I was when I had an I.Q. of 70." Much of what Charlie does in the novel is driven by his need to understand himself and build functional relationships, highlighted when he roams the streets of New York City alone: "for a moment I brush against someone and sense the connection."

A significant theme in the novel is Charlie's attempt to comprehend and reconcile with the people who have hurt him throughout his life: his abusive mother; his father, who failed to protect him; his brutal coworkers at the bakery; and the scientists who raised his intelligence but treated him as a test subject. When Charlie realizes the effects of the operation are temporary, his primary goal becomes finding his family and making peace with them. Upon finding his mother, he tells himself, "I must understand the way she saw it. Unless I forgive her, I will have nothing." The tragedy of Charlie's decline from genius is somewhat alleviated by his reconciliation with those who mistreated him. In his final progress report, he writes, "if they make fun of you don't get sore because you remember their not so smart like you once thot they were."

Although the novel doesn't primarily focus on sexual themes, it does address Charlie's sexual repression stemming from an abusive childhood. His mother, fearing that her "retarded" son might harm his "normal" sister, harshly suppressed any normal adolescent sexual behaviors. As an adult, once Charlie's intelligence improves to the point where he can grasp these complexities, he initially struggles to form a sexual relationship with Fay Lillman, a neighbor who seeks his company. He also finds it challenging to engage in a physical relationship with Alice Kinnian, whom he loves. Charlie's eventual ability to be intimate with Fay and, later, with Alice, signifies a crucial step in overcoming his past traumas and becoming a fully functional adult.