Eye contact plays an essential role in social interaction. Atypical eye contact is a diagnostic and widely reported feature of autism spectrum disorder (ASD). Here, we determined whether altered unconscious visual processing of eye contact might underlie atypical eye contact in ASD. Using continuous flash suppression (CFS), we found that typically developing (TD) adolescents detected faces with a direct gaze faster than faces with an averted gaze, indicating enhanced unconscious processing of eye contact. Critically, adolescents with ASD did not show different durations of perceptual suppression for faces with direct and averted gaze, suggesting that preferential unconscious processing of eye contact is absent in this group. In contrast, in a non-CFS control experiment, both adolescents with ASD and TD adolescents detected faces with a direct gaze faster than those with an averted gaze. Another CFS experiment confirmed that unconscious processing of non-social stimuli is intact for adolescents with ASD. These results suggest that atypical processing of eye contact in individuals with ASD could be related to a weaker initial, unconscious registration of eye contact.