Evidence-based practice (EBP), an approach to clinical practice that places emphasis on the use of best available research evidence for decision-making, has been adopted broadly in clinical practice. As a patient-focused approach, EBP promotes the spirit of inquiry. It can also facilitate consistency of care across professional boundaries, and clarify the directions of research. However, over-emphasis on systematic reviews and randomised control trials as the “gold standard” for evidence is a major limitation of EBP as it is being practised today. There are also objections to EBP based on epistemological grounds. Complementary and alternative medicine (CAM) therapies often fare unfavourably under the scrutiny of EBP due to the lack of research and inherent differences in healing ideology. Naturopathy is a unique form of CAM, based on both traditional and scientific knowledge. We argue that there is no conflict between naturopathy and EBP. EBP can be adopted as a useful approach to assimilate scientific evidence in naturopathic practices. However, naturopaths need to reconcile tensions between traditional and scientific knowledge in their choice of treatment remedies, while adhering to the naturopathic principles of healing, to benefit the patients. They must also maintain their emphasis on clinical expertise, and also patient preferences and values, in clinical decision-making.