One of the keys to preventing a re-emergence of the COVID-19 pandemic is the attainment and maintenance of high vaccination coverage in urban and rural areas. To estimate the coverage of COVID-19 vaccination in a rural population and identify the determinants of vaccination. A cross-sectional survey was conducted in April 2023 in 5 rural districts of Sindh Province, Pakistan. From each district, 30 clusters (villages) were randomly selected, and 7 households were randomly sampled from each cluster using the 30/7 technique. Household members above 12 years of age were included. Vaccination status was categorized as non-vaccinated, partially vaccinated (either with 1 dose or without booster) and completely vaccinated (2 doses with 1 booster). Adjusted odds ratios with 95% confidence intervals using multinomial logistic regression were computed to determine the factors associated with partial and complete vaccination. Data was analysed using SPSS version 20. Among the 3545 individuals surveyed across 1050 households, 25.9% were not vaccinated, 55.0% were partially vaccinated, and 19.1% were fully vaccinated. Younger age, lack of formal education and residing in flood-affected districts were significantly negatively associated with being vaccinated, while living at <5 km from a vaccination facility was significantly positively associated with partial and complete vaccination. Residents of Dadu (OR=0.03, 95% CI=0.01-0.04), Jamshoro (OR=0.05, 95% CI=0.03-0.08), Hyderabad (OR=0.03, 95% CI=0.02-0.05), and Tando Allahyar (OR=0.09, 95% CI=0.05-0.15) districts were significantly less likely to be completely vaccinated than those in Tharparkar. The most common reasons for not being vaccinated were, the perception that COVID-19 is mild (34.5%), fear of side-effects (22.7%), unavailability of the vaccine (19.8%), and fear of acquiring COVID-19 infection through the vaccine (15.8%). Vaccination coverage was low in some of the districts, particularly the flood-affected districts, mainly due to certain myths. There is a need for community outreaches to debunk myths about COVID-19 vaccination among these rural populations.