This study evaluates the propagation impact of three risk categories (hazard and exposure, socio-economic vulnerability, and lack of coping capacity) and their associated factors on vaccination uptake policy decisions in Pakistan. This study proposed Bayesian influence diagrams using expert elicitation and data-driven approaches. The Bayesian network (BN) approach uses the best policy algorithm to determine the expected utility of decisions. The study found that the government’s firm vaccine uptake decisions had a positive effect in Pakistan. The findings on hazard and exposure-related factors show that people living in rural areas were more susceptible to COVID-19 than people living in urban areas. Among socio-economic vulnerability factors, household characteristics were affected due to household economic situations, fear of using health facilities due to the spread of COVID-19, lack of public transportation services, food insecurity, a temporary halt in education, and weak governance, which affected the vaccination uptake decision. The factors linked with coping capacity show that the government’s financial assistance and development of digital platforms raised digital health literacy and increased vaccine uptake decision utility. The proposed methodology and results of this study can be used to develop contingency planning for any future potential pandemic situations.