Public mental health systems play an important role in caring for youth with autism spectrum disorder. Like other dually diagnosed populations, youth with autism spectrum disorder may receive services in the context of evidence-based practice implementation efforts within public mental health systems. Little is known about service use patterns within the context of system-driven implementations efforts for this population. This case-control study examined mental health service patterns of 2537 youth with autism spectrum disorder compared to 2537 matched peers receiving care in the Los Angeles County Department of Mental Health, the largest public mental health department in the United States, within the context of a system-driven implementation of multiple evidence-based practices. Although not the primary target of this implementation effort, youth with autism spectrum disorder were served when they met criteria for the services based on their presenting mental health symptoms. Comparative analyses using administrative claims data were conducted to examine differences in mental health utilization patterns and clinical characteristics. Findings revealed significant differences in the volume and duration of mental health services as well as differences in the service type and evidence-based practice delivered between youth with and without autism spectrum disorder. Results provide direction targeting implementation efforts for youth with autism spectrum disorder within a public mental health system care reform.