The aim of this study was to compare the rates of psychotropic medication use and psychotropic polypharmacy between autistic adults with and without intellectual disability (ID) and to examine factors associated with psychotropic medication use and psychotropic polypharmacy in autistic adults, stratified by the presence of ID. We conducted a retrospective medical chart review of outpatients with an autism diagnosis aged 18 years and older. The rates of psychotropic medication use and psychotropic polypharmacy were compared between autistic adults with and without ID. Subsequently, logistic regression analyses were performed to identify factors associated with psychotropic medication use and psychotropic polypharmacy in autistic adults with ID and those without ID, respectively. The rates of prevalence of psychotropic medication use and polypharmacy were significantly higher in participants with ID than those without ID (78.6% vs. 58.8% and 49.3% vs. 31.2%; p-values < 0.05). Age, gender, race, residence, presence of mood disorders, presence of schizophrenia, absence of anxiety disorder, number of psychiatric comorbidities, and presence of behaviors that challenge were significantly associated with these outcomes, depending on the presence/absence of ID. The need to optimize pharmacotherapy in autistic adults, stratifying by the presence of ID, is highlighted.