Objectives Research is an important tool for sustainable development and the advancement of health. In Bhutan, the need for strengthening the national health research effort has been recognized only in recent years. As a part of research capacity building, this study was conducted to assess the knowledge, attitude and practices of the country’s health care professionals towards research. Methods This was a nationwide cross-sectional study. Simple random sampling was used to obtain a proportionate composition of health professionals. A self-administered questionnaire was developed to assess knowledge through 10 multiple-choice questions, attitude through rating statements, and practices through assessing experiences with research. Knowledge was scored out of 10. Besides analysing proportions, correlation and simple linear regression coefficients were calculated to assess the association of knowledge score with age, work experience, qualification, and the number of research projects undertaken. Results A total of 420 valid questionnaires were collected (response rate = 95.2%). The mean knowledge score was 6.2 (±2.0) out of 10. There was a negative correlation between the knowledge score and the participant’s age (r = –0.15, p = 0.002) and work experience (r = –0.17, p < 0.001). Participants’ knowledge score increased by 0.58 (95% CI: 0.50–0.65, p < 0.001) for each unit increase in qualification level and by 0.75 (95%CI: 0.64–0.87, p < 0.001) for every research project conducted. The majority believed that local research would contribute to better clinical decision making (92.8%) by building local evidence (90.3%). Four out of five participants expressed interest in conducting research. However, only 27.4% had ever conducted research, 6.0% had published in journals and 4.3% had presented in scientific conferences. Less than half of the respondents had read (35.2%) or participated in discussions (42.1%) of research articles in their workplace. The major challenges were lack of knowledge (61.2%), time (49.9%) and resources to undertake literature searches (42.6%). Conclusions Self-reported knowledge about health research was fair, and the conduct of research and utilization of research articles were poor. However, the majority hold positive attitudes and there is a need for supporting professional development in this area.