Children with autism spectrum disorder are prescribed various medications to address behavior and mood. In clinical trials, individuals taking concomitant psychotropic medications often are excluded to maintain homogeneity and prevent contamination of clinical endpoints. However, this choice may compromise the representativeness of the sample. In a recent study designed to identify biomarkers and endpoints for clinical trials (the Autism Biomarkers Consortium for Clinical Trials), school-age children with autism spectrum disorder were enrolled without excluding for medications, providing the opportunity to examine characteristics of psychotropic medication use and guide future decisions on medication-related inclusion criteria. The aims of the current analysis were (1) to quantify the frequency and type of psychotropic medications reported in school-age children enrolled in the study and (2) to examine behavioral features of children with autism spectrum disorder based on medication classes. Of the 280 children with autism spectrum disorder in the cohort, 42.5% were taking psychotropic medications, with polypharmacy in half. The most commonly reported psychotropic medications included melatonin, stimulants, selective serotonin reuptake inhibitors, alpha agonists, and antipsychotics. Our findings suggest that exclusion of children taking concomitant psychotropic medications could limit the representativeness of the study population, perhaps even excluding children who may most benefit from new treatment options.