It is suggested that Charlie dies at the end of the short story "Flowers for Algernon" (as well as the novel of the same novel), as he is following the same process as Algernon, the mouse. Algernon dies after his motor activity slows and he loses coordination. A dissection after death shows that the mouse's brain had lost weight. Charlie realizes at the time that Algernon and he are both subject to the Algernon-Gordon Effect, which is the idea that intelligence that is increased artificially slows down at a rate that is proportional to the increase. That is, as Charlie's intelligence improved rapidly, he will inevitably lose intelligence quickly.

At the end of the short story version of "Flowers for Algernon," Charlie is showing all the signs of decline that Algernon the mouse did. He loses coordination, and he begins to slow down. He also loses the intelligence that he had gained and shows signs of decline, suggesting that he will die. At the end of the novel, Charlie returns to the Warren Home School, and, in his last letter, he asks someone to put flowers on Algernon's grave, also suggesting that he knows he is going to die soon.