Various organizations have endeavored to develop assessment methods for the identification and management of weaknesses in hospital disaster preparedness. Although the largest number of patients receive their regular care at the primary level, there is no internationally validated tool for the rapid safety assessment of primary health care centers (PHC). Flooding accounts for almost 50% of all disasters related to weather, and climate models consider these events as highly probable in the future. In May 2014, heavy rain caused floods affecting around 1.6 million people in Serbia, leaving the municipality of Obrenovac most severely impacted. This paper aims at assessing the safety of PHC Obrenovac using the Hospital Safety Index (HSI), evaluating the usefulness of HSI for safety assessment of PHCs, and drawing lessons from the 2014 floods. PHC Obrenovac had an overall safety index of 0.82, with structural, nonstructural safety, and disaster management indices of 0.95, 0.74, and 0.75, respectively, implying it is likely to function in disasters. A detailed analysis of individual HSI items underlined the necessary improvements in the field of emergency power and water supply, telecommunication, and emergency medical supplies, which rendered the PHC non-functional during the 2014 floods. Most items were considered of same relevance for primary healthcare centers as for hospitals, excluding some items in the medical equipment, patient care, and support services. Fine-tuning the HSI to primary healthcare settings, officially translating it into different languages, facilitating scoring and analysis could result in a valid safety evaluation tool of primary healthcare facilities.