The Juvenile Justice (JJ) system has a number of local behavioral health service community linkages for substance abuse, mental health, and HIV services. However, there have only been a few systemic studies that examine and seek to improve these community behavioral health linkages for justice-involved youth. Implementation research is a way of identifying, testing, and understanding effective strategies for translating evidence-based treatment and prevention approaches into service delivery. This article explores benefits and challenges of participatory research within the context of the National Institute on Drug Abuse (NIDA)’s Juvenile Justice Translational Research on Interventions for Adolescents in the Legal System (JJ-TRIALS) implementation behavioral health study. The JJ-TRIALS study has involved JJ partners (representatives from state-level JJ agencies) throughout the study development, design, and implementation. Proponents of participatory research argue that such participation strengthens relations between the community and academia; ensures the relevancy of research questions; increases the capacity of data collection; and enhances program recruitment, sustainability, and extension. The extent of the impact that JJ partners have had on the JJ-TRIALS study will be discussed, as well as the benefits local JJ agencies can derive from both short- and long-term participation. Issues associated with the site selection, participation, and implementation of evidence-based practices also will be discussed.