Undocumented pregnant women migrants and their young children are disproportionately affected by displacement and health system constraints. In Thailand, chronic gaps in financing and manpower resources challenge the sustainability of border health facilities to provide services to migrants. Kanchanaburi has a high proportion of irregular migrants from Myanmar, and also one of the highest reported proportions of unpaid health expenses by migrants compared to other provinces in Thailand. Using both implementation science and system dynamics approaches, and drawing upon lessons from Tak province, a multi-layered evidence base for designing resilient interventions in Kanchanaburi is generated in this study. The study identified gaps in maternal, newborn and child health (MNCH) among undocumented migrants in Kanchanaburi, and provided recommendations for multi-stakeholder collaboration and advocacy to strengthen MNCH care.