Background Despite significant investment, mental health issues remain a leading cause of death among young people globally. Sophisticated decision analysis methods are needed to better understand the dynamic and multisector drivers of youth mental health. System modeling can help explore complex issues such as youth mental health and inform strategies to effectively respond to local needs and achieve lasting improvements. The advantages of engaging stakeholders in model development processes have long been recognized; however, the methods for doing so are often not well-described. Objective This paper aims to describe the participatory procedures that will be used to support systems modeling for national multisite implementation. The Right Care, First Time, Where You Live research program will focus on regional youth mental health applications of systems modeling in 8 different sites across Australia. Methods The participatory model development approach involves an iterative process of engaging with a range of participants, including people with lived experience of mental health issues. Their knowledge of the local systems, pathways, and drivers is combined with the academic literature and data to populate the models and validate their structure. The process centers around 3 workshops where participants interact and actively engage in group model-building activities to define, refine, and validate the systems models. This paper provides a detailed blueprint for the implementation of this process for mental health applications. Results The participatory modeling methods described in this paper will be implemented at 2 sites per year from 2022 to 2025. The 8 selected sites have been chosen to capture variations in important factors, including determinants of mental health issues and access to services. Site engagement commenced in August 2021, and the first modeling workshops are scheduled to commence in February 2022. Conclusions Mental health system decision makers require tools to help navigate complex environments and leverage interdisciplinary problem-solving. Systems modeling can mobilize data from diverse sources to explore a range of scenarios, including the impact of interventions in different combinations and contexts. Involving stakeholders in the model development process ensures that the model findings are context-relevant and fit-for-purpose to inform decision-making. International Registered Report Identifier (IRRID) PRR1-10.2196/32988