Background: Floods affect over 85 million people every year and are one of the deadliest types of natural disasters. The health effects of floods are partly due to a loss of access to health care. This loss can be limited with proper flood preparedness. Flood preparedness is especially needed at the primary health care (PHC) level. Flood preparedness assessments can be used to identify vulnerable facilities and help target efforts. The existing research on PHC flood preparedness is limited. We aimed to assess the flood preparedness of PHC facilities in a flood-prone province in central Vietnam. Methods: Based on flood experience, the PHC facilities in the province were grouped as "severe" (n = 23) or "non-severe" (n = 129). Assessments were conducted during monsoon season at five facilities from each group, using a pre-tested, semi-structured questionnaire. Data were checked against official records when possible. Results: Nine of the ten facilities had a flood plan and four received regular flood preparedness training. Six facilities reported insufficient preparedness support. Half of the facilities had additional funding available for flood preparedness, or in case of a flood. Flood preparedness training had been received by 21/28 (75%) of the staff at the facilities with severe flood experience, versus 15/25 (52%) of the staff at the non-severe experience facilities. Conclusions: Our results suggest that the assessed PHC facilities were not sufficiently prepared for the expected floods during monsoon season. PHC flood preparedness assessments could be used to identify vulnerable facilities and populations in flood-prone areas. More research is needed to further develop and test the validity and reliability of the questionnaire.