The youth mental health sector is persistently challenged by issues such as service fragmentation and inefficient resource allocation. Systems modelling and simulation, particularly utilizing participatory approaches, is offering promise in supporting evidence-informed decision making with limited resources by testing alternative strategies in safe virtual environments before implementing them in the real world. However, improved evaluation efforts are needed to understand the critical elements involved in and to improve methods for implementing participatory modelling for youth mental health system and service delivery. An evaluation protocol is described to evaluate the feasibility, value, impact, and sustainability of participatory systems modelling in delivering advanced decision support capabilities for youth mental health. This study applies a comprehensive multi-scale evaluation framework, drawing on participatory action research principles as well as formative, summative, process, and outcome evaluation techniques. Novel data collection procedures are presented, including online surveys that incorporate gamification to enable social network analysis and patient journey mapping. The evaluation approach also explores the experiences of diverse stakeholders, including young people with lived (or living) experience of mental illness. Social and technical opportunities will be uncovered, as well as challenges implementing these interdisciplinary methods in complex settings to improve youth mental health policy, planning, and outcomes. This study protocol can also be adapted for broader international applications, disciplines, and contexts.