Close phenotypic characterization of individuals with genetic conditions linked to autism provides a promising approach to navigating the heterogeneity of autism spectrum conditions. The current study investigated sensory processing in individuals with a rare genetic event that is highly penetrant for autism, 16p11.2 deletions, using a well‐characterized visual paradigm, binocular rivalry, which is thought to be a non‐invasive index of excitatory/inhibitory balance in the visual cortex. We characterized rivalry dynamics in 45 adolescent and adult individuals (19 individuals with 16p11.2 deletions, 26 age‐matched neurotypical controls). We found that binocular rivalry perceptual transition rates were significantly slower for individuals with 16p11.2 deletions, relative to controls. Importantly, these results could not be accounted for by differences in motor response latencies or perceptual decision criteria, which were matched between groups. Results should be interpreted with caution given the unmatched psychometric features between groups, such as IQ. Future studies should study visual processing in other genetic groups linked to autism beyond 16p to understand the specificity of these findings. These results highlight the importance of characterizing sensory functions in individuals with genetic alterations associated with autism.