Psychoanalytic psychotherapy and autism have had a complicated relationship. Much of the complication has arisen from patients with autism being misunderstood by those who have used a psychoanalytic lens. These misunderstandings arose not for a lack of trying—but rather from a disavowal of how neurological difference shapes what it means to become a person, and how these differences affect treatment needs. It has been autistic patients who have had to bear the consequences of these misunderstandings in much the same way as they do in their daily lives outside of therapy. It is not the psychoanalytic lens that has failed these patients, but rather its use without reference to the ever-growing body of neurobiological knowledge. In this paper, we make the argument that many of the key psychoanalytic concepts—countertransference, the frame, narcissism, intellectualization and obsessions—need to be reviewed and altered when working with autistic patients.