Kemper had a dark fantasy life. He performed rites with his younger sister's dolls that culminated in his removing their heads and hands; and on one occasion, when his elder sister, Susan Hughey Kemper (1943–2014), teased him and asked why he did not try to kiss his teacher, he replied, "If I kiss her, I'd have to kill her first." He also recalled that as a young boy, he would sneak out of his house and, armed with his father's bayonet, go to his second-grade teacher's house to watch her through the windows. He also had near-death experiences as a child: once, when his elder sister tried to push him in front of a train and another time when she successfully pushed him into the deep end of a swimming pool, where he almost drowned.
Kemper had a close relationship with his father and was devastated when his parents separated in 1957, causing him to be raised by his mother Clarnell in Helena, Montana. He had a severely dysfunctional relationship with his mother, a neurotic, domineering alcoholic who frequently belittled, humiliated, and abused him. Clarnell often made her son sleep in a locked basement because she feared that he would harm his sisters, regularly mocked him for his large size—he stood 6 feet 4 inches (1.93 m) by the age of 15—and derided him as "a real weirdo." She also refused to show him affection out of fear that she would "turn him gay" and told the young Kemper that he reminded her of his father and that no woman would ever love him. Kemper later described her as a "sick angry woman".