Background: Evidence based practice (EBP) requires that health professionals are competent in integrating the best evidence in their decision making. Being 'evidence-based' requires skills and knowledge in epidemiology, biostatistics and information literacy. EBP is commonly taught in medical and health sciences degrees, yet there is little evidence to guide educators as to the best teaching modality to increase learner competency in EBP. Methods/design. This study is mixed methods in design. A randomised controlled trial will examine the effectiveness of blended learning versus didactic approach of teaching EBP to medical students. The primary outcome of the RCT is EBP competency as assessed by the Berlin tool. Focus groups will be conducted to explore student perceptions and attitudes towards implementing a blended learning approach in teaching EBP. A concurrent triangulation design will be implemented, permitting quantitative data to inform the effectiveness of the intervention and qualitative data to contextualise the results. Discussion. This study will provide novel evidence on the effectiveness of blended learning in teaching EBP to a cohort of undergraduate and graduate-entry medical students.