Charlie is the central protagonist of the story, a unique fifteen-year-old boy living in Missouri who is the world's only humanzee, a hybrid being born from human DNA and a chimpanzee. His origin traces back to a raid by the Animal Liberation Alliance, an extremist animal rights organization, on a bioscience research institute where a pregnant chimpanzee was rescued. This chimpanzee, named Eva, gave birth to Charlie, though he was subsequently raised by a human couple, his adoptive parents Gilbert and Hannah, and has little emotional connection to his biological mother. Charlie possesses a combination of abilities that set him apart from both humans and animals, including physical strength that exceeds that of a chimpanzee, capable of gripping six hundred times his own weight, and an intelligence that surpasses that of humans.

In terms of personality, Charlie is generally calm, self-assured, and detached, often regarding events and the people around him with a dry, logical evaluation. Having had almost no interaction with anyone other than his parents before entering high school, he can occasionally say or do things that astonish those around him, as he is still learning the nuances of social behavior. His thinking is pragmatic and unfiltered; when a bully poses a hypothetical question about killing a diseased mouse to save his own life, Charlie calmly responds that he would have no issue shooting the bully if he were carrying a life-threatening illness. Despite this seemingly cold logic, he shows an inherent inclination toward kindness, demonstrated when he crashes through a window to rescue a girl and a cat from a fall or when he plucks a butterfly from a spider's web.

Charlie's primary motivation throughout the story is to protect the people he cares about, specifically his adoptive family and his new friend Lucy, a sharp-minded but socially isolated girl he meets at school. Because of his unique identity, the Animal Liberation Alliance attempts to recruit him as a symbol for their cause, but Charlie chooses to oppose the organization directly in order to defend his loved ones. In the course of the story, he also travels to New York to find a scientist named Dr. Grossman, seeking answers about his own origins.

His relationship with Lucy is central to his development. She is one of the first people his age to treat him as something other than a spectacle, and their bond grows as they face the challenges of discrimination, terrorism, and social conflict together. Their communication is unique; Charlie often gives slightly off-kilter answers that Lucy interprets by watching his subtle eye movements and reactions, and this dynamic creates a connection that the original creator describes as one where two different beings try to understand each other while accepting that complete understanding may not be necessary. Through his interactions with Lucy, Charlie begins to change and develop, though his emotions are often difficult to read. At the same time, he displays a cold indifference toward his biological mother, the chimpanzee Eva, referring to her merely as his biological mother and showing no sentimental attachment. His existence forces the humans around him to reconsider their ethical relationships with animals, technology, and life itself, and he poses fundamental questions to human civilization, such as why humans are the only beings that cannot be killed and eaten.