Functional MRI typically makes inferences about neural substrates of cognitive phenomena at the group level. We report the use of a single-stimulus blood-oxygen-level-dependent (BOLD) response in the cingulate cortex that differentiates individual children with autism spectrum disorder from matched typically developing control children with sensitivity and specificity of 63.6 and 73.7, respectively. The approach consists of passive viewing of self and other faces from which an individual difference measure is derived from the BOLD response to the first self-face image only. The method, penalized logistic regression, requires no averaging over stimulus presentations or individuals. These findings show that single-stimulus functional MRI responses can be extracted from individual subjects and used profitably as a neural individual difference measure. The results suggest that single-stimulus functional MRI can be developed to produce quantitative neural biomarkers for other developmental disorders and may even be useful in the rapid typing of cognition in healthy individuals.