Body image disturbance is a key symptom of anorexia nervosa (AN). AN patients report body dissatisfaction and overestimate their own body size in several tasks. This study aimed to clarify whether this overestimation arises from deficits in visual perception. To this end, 36 adolescent restrictive-type AN patients and 42 matched healthy controls performed metric and depictive body size estimation (BSE) tasks. Magneto- and electroencephalography were measured during the size estimation of 66 computer-generated body pictures varying in size from underweight to overweight. AN patients versus controls showed overestimation across self-referential metric and depictive BSE tasks, but similar performance in a depictive BSE task without self-reference and similar early neurophysiological responses. Starting mid-latency (200 ms), AN patients showed relatively more neural activity in response to underweight body pictures and less neural activity in response to higher-weight body pictures in distributed brain regions. A secondary comparison of AN patients with slight vs. distinct overestimation during self-referential BSE uncovered relatively stronger neural responses to body pictures corresponding to the estimated body mass index. These results suggest that body image disturbances in adolescent restrictive-type AN patients depend on self-reference and do not represent a deficit of visual perception, but rather biased emotional attention.