Objective There is an evolving debate about pathological affective responses in patients with anorexia nervosa (AN). We examined startle responses in different stages of AN. Methods We applied a startle reflex paradigm with standardized visual stimuli (International Affective Pictures System; food and body pictures) in 64 female participants (17 acute AN, 16 chronically ill AN, 15 long‐term recovered AN, 16 healthy controls). We measured subjective ratings of valence and anxiety, and electromyographic startle responses. Results Participants with acute and chronic AN displayed the same subjective valence ratings to affective stimuli but showed less startle reactivity to affective pictures (F(6, 116) = 2.75, p = .02) compared with healthy control. Food pictures were rated as more unpleasant and higher anxiety provoking by currently ill AN (F(3, 59) = 3.32, p=.03). Discussion We observed diverging subjective and psychophysiological reactions in different stages of AN. Psychophysiological methods can help to attain a more comprehensive understanding of biological alterations in the long‐term course of AN. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.