Background: Evidence-based medicine is the integration of individual clinical expertise, best external evidence and patient values which was introduced more than two decades ago. Yet, primary care physicians in Malaysia face unique barriers in accessing scientific literature and applying it to their clinical practice. Aim: This study aimed to explore the views and experiences of rural doctors' about evidence-based medicine in their daily clinical practice in a rural primary care setting. Methods: Qualitative methodology was used. The interviews were conducted in June 2013 in two rural health clinics in Malaysia. The participants were recruited using purposive sampling. Four focus group discussions with 15 medical officers and three individual in-depth interviews with family medicine specialists were carried out. All interviews were conducted using a topic guide and were audio-recorded, transcribed verbatim, checked and analyzed using a thematic approach. Results: Key themes identified were: (1) doctors viewed evidence-based medicine mainly as statistics, research and guidelines, (2) reactions to evidence-based medicine were largely negative, (3) doctors relied on specialists, peers, guidelines and non-evidence based internet sources for information, (4) information sources were accessed using novel methods such as mobile applications and (5) there are several barriers to evidence-based practice, including doctor-, evidence-based medicine-, patient- and system-related factors. These included inadequacies in knowledge, attitude, management support, time and access to evidence-based information sources. Participants recommended the use of online services to support evidence-based practice in the rural settings. Conclusion: The level of evidence-based practice is low in the rural setting due to poor awareness, knowledge, attitude and resources. Doctors use non-evidence based sources and access them through new methods such as messaging applications. Further research is recommended to develop and evaluate interventions to overcome the identified barriers.