Despite the significance of health and the threats natural disasters pose to public health and the well-being of the affected communities, comprehensive research that explores critical factors and indicators that measure health implications brought about by disasters is underdeveloped in the literature. The primary objective of this study is twofold: (1) to develop a list of indicators that assess health-related impacts during disasters through a literature survey, and (2) to create a “public health resilience index” that measures the resilience of affected communities with a case study in Southern Cebu, Philippines. A hybrid model based on the fuzzy stepwise weight assessment ratio analysis and the extended cumulative prospect theory was deployed to advance these objectives. The proposed model considers subjective judgment and cognitive biases while exhibiting high scalability and flexibility and accommodating diverse data input formats. Results revealed that the promptness of response, the allocated budget for humanitarian aid and services, the availability of drinking water per household, the number of personnel assigned for humanitarian aid, and the location of water distribution points are highly prioritized during natural disasters. On the other hand, among the 21 municipalities under consideration, 10 demonstrated strong performance, while the other 10 exhibited poor performance, leaving one municipality in the middle of both extremes. Sensitivity and comparative analyses show that the proposed hybrid model is not sensitive to model parameter changes. The findings of this study would aid decision-makers in developing initiatives aimed at optimizing resources and efforts, mitigating risks, and enhancing the overall health resilience of local communities in the onslaught of natural disasters.