Background Delivery of behavioral interventions is complex, as the majority of interventions consist of multiple components used either simultaneously, sequentially, or both. The importance of clearly delineating delivery strategies within these complex interventions - and furthermore understanding the impact of each strategy on effectiveness - has recently emerged as an important facet of intervention research. Yet, few methodologies exist to prospectively test the effectiveness of delivery strategies and how they impact implementation. In the current paper, we describe a study protocol for a large randomized controlled trial in which we will use the Multiphase Optimization Strategy (MOST) – a novel framework developed to optimize interventions - to test the effectiveness of intervention delivery strategies using a factorial design. We apply this framework to delivery of Family Navigation (FN), an evidence-based care management strategy designed to reduce disparities and improve access to behavioral health services, and test four components related to its implementation. Methods/Design The MOST framework contains three distinct phases: Preparation, Optimization, and Evaluation. The preparation phase for this study occurred previously. The current study consists of the optimization and evaluation phases. Children ages three-to-twelve years-old who are detected as “at-risk” for behavioral health disorders (n=304) at a large, urban federally qualified community health center will be referred to a Family Partner – a bi-cultural, bi-lingual member of the community with training in behavioral health and systems navigation – who will perform FN. Families will then be randomized to one of 16 possible combinations of FN delivery strategies (2x2x2x2 factorial design). The primary outcome measure will be achieving a family-centered goal related to behavioral health services within 90 days of randomization. Implementation data on fidelity, acceptability, feasibility, and cost of each strategy will also be collected. Results from the primary and secondary outcomes will be reviewed by our team of stakeholders to optimize FN delivery for implementation and dissemination based on effectiveness, efficiency, and cost. Discussion In this protocol paper, we describe how the MOST Framework can be used to improve intervention delivery. These methods will be useful for future studies testing intervention delivery strategies and their impact on implementation.