Recognizing gender-based violence (GBV) as a serious public health problem, the Domestic Violence Prevention Act of Bhutan was enacted in 2013 that mandates the Ministry of Health to establish appropriate facilities with trained health professionals to provide care for the survivors of domestic violence. Although health facilities in the country provide services to the survivors of GBV, there is limited information on the quality of care and burden of survivors availing services at health-care facilities in Bhutan. The assessment was conducted in 70 health facilities in 20 districts. A self-administered questionnaire and facility assessment checklist were used to collect the quantitative data. Data were analyzed using SPSS. Key informants' interviews were conducted with relevant officials and findings were analyzed qualitatively using the content analysis method. A total of 1557 GBV cases were reported in health facilities in a year and 80% were reported to regional and district hospitals (n = 1257). Of those who received medical care, 68% of GBV survivors were women. Eighty-six percent of health-care professionals who provided care did not receive any training on GBV management. We conclude that there is an urgent need to develop national guidelines and train health workers regarding health system and health-care responses to GBV, including streamlining the data collection and storage at health facilities.