BACKGROUND: Multidrug-resistant tuberculosis (MDR-TB) is a growing public health concern globally. In Bhutan, the rates of MDR-TB are high. Data on the risk factors of MDR-TB that can help inform policies are limited in Bhutan. This study aimed to determine the risk factors associated with MDR-TB. METHODS: A nationwide unmatched case-control study was conducted that included 79 MDR-TB cases and 118 controls. Data was collected by trained health workers through interviews using a structured questionnaire. Logistic regression analysis was performed to identify the risk factors associated with MDR-TB. RESULTS: The mean age of the participants was 32.4 and 33.7 years among the cases and the controls, respectively. In the multivariate analysis, the odds of having MDR-TB was higher among those who slept for less than 9 hours a day (AOR: 2.77, 95%CI: 1.11-6.92), frequently travelled in public transport (AOR: 2.96, 95% CI: 1.36-6.48), and had previous TB treatment (AOR: 5.90, 95%CI: 2.55-13.64). A greater number of rooms was also marginally associated with odds of having MDR-TB. CONCLUSIONS: The findings suggest previous TB treatment, inadequate sleep duration, and travelling by public transport to be the risk factors associated with having MDR-TB in Bhutan. Intensification of early case detection, strengthening directly observed treatment strategy, improving treatment adherence, and increasing awareness can help control the rising MDR-TB epidemic.