Background The migrant health agenda in Thailand has been shaped by domestic and international pressures relating to social and economic dimensions. Thailand has become a popular destination for international migrant workers particularly from Cambodia, Lao PDR, and Myanmar. However, only a fraction of these migrant workers were insured by public health insurance. This study aimed to apply systems thinking to explore contextual factors affecting access to public health insurance arrangements among cross-border migrants in Thailand. Methods A group model building (GMB) was applied to explore contextual factors and their interplay influencing access to health insurance for migrants in Thailand. Participants (n = 20) were encouraged to share ideas about underlying drivers and barriers of access to health insurance among migrants. Triangulation was performed with the document review. The findings were analysed by a thematic approach. The causal loop diagramme (CLD) and stock and flow diagramme (SFD) were synthesised to identify the dynamics relating to access to migrant health insurance. Results Nationality verification was recognised as one of the most important mechanisms that the Thai government exercises to deal with the precarious citizenship status of undocumented migrants. Also, it is the key function that links economic necessity, national security, and public health concerns. In the formal sector, the government plays an important role in the enrollment of migrant workers in the Social Security Scheme (SSS) run by the Ministry of Labour (MOL). In the informal sector, the Health Insurance Card Scheme (HICS) managed by the Ministry of Public Health (MOPH) is the key option for migrant workers. However, some migrants are still left uninsured. The likely explanations are the semi-voluntary nature of the HICS, administrative delay of the enrollment process, and the resistance of some employers to hiring migrants. Conclusions Effective communication is required to raise awareness and acceptance towards the insurance among migrants and their employers. This needs cohesive effort from all stakeholders in society including the government, the business sector, civic groups, and even migrant communities. A public policy participatory process is needed to create a good balance of migrant policies among diverse authorities.