Background Dengue has emerged as a major public health problem in Bhutan, with increasing incidence and widening geographic spread over recent years. This study aimed to investigate the knowledge and clinical management of dengue among medical practitioners in Bhutan. Methods We administered a survey questionnaire to all practitioners currently registered under the Bhutan Medical and Health Council. The questionnaire contained items on four domains including transmission, clinical course and presentation, diagnosis and management, and surveillance and prevention of dengue. Participants were able to respond using an online Qualtrics survey, with the invitation and link distributed via email. Results A total of 97 respondents were included in the study (response rate: 12.7%), of which 61.86% were Health Assistants/Clinical Officers (HAs/COs) and 38.14% were medical doctors. The afternoon feeding behaviour of Aedes mosquito was correctly identified by only 24.7% of the respondents, and ~66.0% of them failed to identify lethargy as a warning sign for severe dengue. Knowledge on diagnosis using NS1 antigen and the clinical significance of elevated haematocrit for initial fluid replacement was strikingly low at 47.4% and 27.8% respectively. Despite dengue being a nationally notifiable disease, ~60% of respondents were not knowledgeable on the timing and type of cases to be reported. Respondent's median score was higher for the surveillance and reporting domain, followed by their knowledge on transmission of dengue. Statistically significant factors associated with higher knowledge included respondents being a medical doctor, working in a hospital and experience of having diagnosed dengue. Conclusion The study revealed major gaps on knowledge and clinical management practices related to dengue in Bhutan. Physicians and health workers working in Basic Health Units need training and regular supervision to improve their knowledge on the care of dengue patients.