Background <p>Flood hazards are increasingly frequent and severe in developing countries, including Pakistan, posing major challenges to primary healthcare delivery. In Khyber Pakhtunkhwa, recurrent floods damage infrastructure, disrupt medical services, and impair the operational readiness of Rural Health Centers, undermining access to care for vulnerable populations. Despite high flood exposure, evidence on Rural Health Center preparedness remains scarce. This study aimed to assess the preparedness level of Rural Health Centers using the Hospital Safety Index in flood-prone districts of Khyber Pakhtunkhwa and to explore the implications for health system resilience and the relevant Sustainable Development Goals.</p> Methods <p>We conducted a cross-sectional quantitative survey across 13 Rural Health Center in four flood-prone districts of Khyber Pakhtunkhwa, Pakistan. A total of 156 healthcare staff members were surveyed using structured interviews based on the World Health Organization Hospital Safety Index to gather data on structural, non-structural, and functional preparedness. Descriptive statistics were used to analyze preparedness indicators. We applied a SWOT (Strengths, Weaknesses, Opportunities, Threats) framework to synthesize institutional capacities and identify gaps, and mapped the findings to relevant Sustainable Development Goals to contextualize the results within broader global health and resilience targets.</p> Results <p>According to the World Health Organization Hospital Safety Index classification, most indicators fell into Category C (0–35%), indicating the need for urgent intervention, while functional power support (41%) reached Category B (36–65%), requiring short-term intervention. Structural preparedness scores averaged 28% for building integrity (range 18–38%) and 30% for evacuation space (range 20–40%), indicating high vulnerability and minimal flood-resistant design. Non-structural preparedness showed critical gaps: medical oxygen continuity (24–26%), back-up power (25%), equipment protection (24–27%), and medicine storage (24–27%). Accessibility averaged 30–32%, with functional power support reaching 41% (the only Category B indicator). Functional preparedness revealed severe weaknesses in human resources and management: designated emergency staff (13%), operational planning (19%), internal coordination (29%), and health committees (27%). Capacity building scores were low: staff training (31%) and emergency drills (29%). Evacuation and coordination indicators averaged 24–26%. Despite these gaps, strengths included safe drinking water (61%), emergency shelter (47%), surge beds (47%), and emergency food (45%). SWOT analysis identified basic service continuity and internal coordination as strengths; weak infrastructure and operational readiness as key weaknesses; opportunities in peer learning, digital logistics, and community engagement; and threats including escalating flood severity, chronic underinvestment, and weak multi-agency coordination.</p> Conclusions <p>Rural Health canters in Khyber Pakhtunkhwa remain critically underprepared for floods across all three preparedness domains. Targeted interventions are urgently needed to strengthen infrastructure resilience, secure non-structural systems, enhance functional capacity, expand emergency training and drills, improve transport and logistics, and foster inter-agency and community coordination. These measures would safeguard health service delivery during floods and support health- and resilience-related SDGs.</p>