Abstract Background Ninety percent of children with mental health problems live in low or middle-income countries (LMICs). School-based programs offer opportunities for early identification and intervention, however implementation requires cross-sector collaboration to assure sustainable delivery of quality training, ongoing supervision, and outcomes monitoring at scale. In Pakistan, 35% of school-aged children are reported to have emotional and behavioral problems. As in many other LMICs, the government agencies who must work together to mount school-based programs have limited resources and a limited history of collaboration. The “Theory of Change” (ToC) process offers a way for new partners to efficiently develop mutual goals and long-term prospects for sustainable collaboration. Objective Develop a model for scale-up of school based mental health services in public schools of Pakistan. Methods We used ToC workshops to develop an empirically supported, ‘hypothesized pathway’ for the implementation of WHO’s School Mental Health Program in the public schools of rural Pakistan. Three workshops included 90 stakeholders such as policy makers from education and health departments, mental health specialists, researchers, head teachers, teachers and other community stakeholders including non-governmental organizations. Results The ToC process linked implementers, organizations, providers and consumers of school mental health services to develop common goals and relate them (improved child socioemotional wellbeing, grades and participation in activities) to interventions (training, monitoring and supervision of teachers; collaboration with parents, teachers and primary health care facilities and schools). Key testable assumptions developed in the process included buy-in from health care providers, education officials and professionals, community-based organizations and families. For example, teachers needed skills for managing children’s problems, but their motivation might come from seeking improved school performance and working conditions. Poverty, stigma and lack of child mental health literacy among teachers, administration, and parents were identified as key hypothesized barriers. Children and their families were identified as key stakeholders to make such a program successful. Discussion ToC workshops assisted in team building and served as a stakeholders’ engagement tool. They helped to develop and support testable hypotheses about the structures, collaborations, and knowledge most important to scaling-up school based mental health services in Pakistan.