Throughout the story Flowers for Algernon, the relationship between Charlie Gordon and his teacher, Miss Kinnian, evolves, progresses, and then regresses by the conclusion of the story. When the story begins, Miss Kinnian is Charlie's teacher at the adult school, and she is also the person who has recommended Charlie as a candidate for the experimental surgery. As Charlie continues to make gains intellectually, Miss Kinnian stays by his side, a constant encouraging influence, and over time Charlie develops romantic feelings for Miss Kinnian. However, as Charlie reaches the pinnacle of his intelligence, he becomes angered by Miss Kinnian while they are out together, stating, "When I tried to explain she stopped me and laughed. I guess I got angry, but I suspect I'm approaching her on the wrong level." Charlie becomes angry because he is sensitive about being laughed at, since he has learned that many laughed at him in his previous state. However, even in the reflection of his journal, Charlie has already realized that Miss Kinnian was not laughing at him to mock him, but because she was uncomfortable with her own lack of understanding, and therefore he does not stay angry with her.

Near the conclusion of the story, Miss Kinnian comes to see Charlie as he is regressing, and he treats her in a way that may make the reader believe that he is angry by stating, "Miss Kinnian came to the door but I said go away I dont want to see you...I told her I didn't like her any more . . . ." Charlie is not really angry with Miss Kinnian at this time, but he pushes her away because he is embarrassed by his regressed state, and he does not want Miss Kinnian to see him this way.