Abnormal fMRI habituation in autism spectrum disorders (ASDs) has been proposed as a critical component in social impairment. This study investigated habituation to fearful faces and houses in ASD and whether fMRI measures of brain activity discriminate between ASD and typically developing (TD) controls. Two identical fMRI runs presenting masked fearful faces, houses, and scrambled images were collected. We found significantly slower fMRI responses to fearful faces but not houses in ASD. In addition, the pattern of slow to emerge amygdala activation to faces had robust discriminability [ASD vs. TD; area under the curve (AUC) = 0.852, p < 0.001]. In contrast, habituation to houses had no predictive value (AUC = 0.573, p = 0.365). Amygdala habituation to emotional faces may be useful for quantifying risk in ASD.