Background: Self-medication is a global phenomenon and a potential contributor to negative health consequences on human health including emergence of antibiotic drug resistance globally. Objective: The primary objective of this study was to estimate the prevalence and determinants of self-medication in Thimphu, Bhutan and Chattogram, Bangladesh, two neighbouring South Asian country. Methodology: A community-based cross-sectional study was conducted in the city of Thimphu, Bhutan and Chattogram, Bangladesh. A pre-tested and semi-structured questionnaire was used to collect information on socio-demographic characteristics, health status and self-medication practices in the previous year. Results: Out of the 998 recruited participants, 61.8% (170/275) from Thimphu and 41.5% (300/723) from Chattogram reported self-medication practices in last year of interview. In Thimphu, eye/ear infection (90.9%), fever (84.9%), headache (80.5%) and cough and cold (78.2%) were the major illnesses reported for self-medication, whereas in Chattogram people mostly self-medicated for skin disorder (74.4%), diarrhoeal illness (59.1%) and eye/ear infection (48.1%). Knowledge on side-effects of the drugs taken for self-medication was comparatively higher in Thimphu than in Chattogram. Both in Thimphu and Chattogram, higher odds of self-medication were found for common illnesses with adjusted OR 7.8; 95% CI 3.3–18.4 and adjusted OR 2.0; 95% CI 1.4–2.8, respectively in Thimphu and Chattogram. Conclusion: Self-medication was found to be substantially high in both the cities, however, rate of self-medication was higher in Thimphu compared to Chattogram. Knowledge and awareness raising about harmful effect of self-medication and effective regulation over selling of prescription medication in pharmacies should be strengthened in both countries.