(1) Background: This qualitative research had the objective to study the reasons for non-acceptance of the COVID-19 vaccination by some Muslims in the three southern border provinces of Thailand; (2) Methods: Data collection was done in a community of Pattani province and communities along the Thai-Malaysian border of Narathiwat province by observation and in-depth interview. The 40 key informants were community Muslims, religious leaders and public health workers selected by purposive sampling according to their knowledge of the situation. The data were tested by triangulation and analytical descriptive conclusion; (3) Results: Some Muslims did not accept the COVID-19 vaccination for six important reasons: 1) The belief that the village health volunteers (VHV) who persuaded them to have vaccination only hoped for the state reward. 2) Death is the will of God so vaccination is not necessary. 3) Every kind of vaccine is not halal. 4) Vaccination is the cause of weakened ability. 5) Vaccination had caused death, and 6) Fear of re-vaccination impact because they had the vaccination in Malaysia. (4) Conclusions Involving religious leaders and fostering Thailand-Malaysia cooperation are key to combating health misinformation. Culturally sensitive health education can improve public health responses in the southern border region.