This study aimed to describe rates of antipsychotic medication use and the association between their use and demographics, clinical variables, and the use of behavioral/education services among children with ASD. For children with ASD ages 2–11 (n = 4749) and those 12–17 (n = 401), 5.4 and 17.7% were prescribed at least one atypical antipsychotic medication respectively. In the multivariable model of young children, older age, use of multiple psychotropic medications, prior ASD diagnosis, non-white Hispanic race/ethnicity, and oppositional defiant problems were associated with antipsychotic use. Among older children, only older age was associated with antipsychotic use. In at least one age group, antipsychotic medication use was also related to behaviour, family and occupational therapy, public insurance, site region, externalizing problems, body mass index, and sleep and gastrointestinal problems.