BackgroundTeaching Evidence Based Medicine (EBM) is becoming a priority in the healthcare process. For undergraduates, it has been proved that integrating multiple strategies in teaching EBM yields better results than a single, short-duration strategy. However, there is a lack of evidence on applying EBM educational interventions in developing countries. In this study, we aim to evaluate the effectiveness of a multiple strategy peer-taught online course in improving EBM awareness and skills among medical students in two developing countries, Syria and Egypt.MethodsWe conducted a prospective study with pre- and post- course assessment of 84 medical students in three universities, using the Berlin questionnaire and a set of self-reported questions which studied the students’ EBM knowledge, attitude and competencies. The educational intervention was a peer-taught online course consisting of six sessions (90 min each) presented over six weeks, and integrated with assignments, group discussions, and two workshops.ResultsThe mean score of pre- and post-course Berlin tests was 3.5 (95% CI: 2.94–4.06) and 5.5 (95% CI: 4.74–6.26) respectively, increasing by 2 marks (95% CI: 1.112–2.888; p-value <0.001), which indicates a statistically significant increase in students’ EBM knowledge and skill, similar to a previous expert-taught face to face contact course. Self-reported confidences also increased significantly. However, our course did not have a major effect on students’ attitudes toward EBM (1.9–10.8%; p-value: 0.12–0.99).ConclusionIn developing countries, multiple strategy peer-taught online courses may be an effective alternative to face to face expert-taught courses, especially in the short term.Electronic supplementary materialThe online version of this article (doi:10.1186/s12909-017-0924-1) contains supplementary material, which is available to authorized users.