E-learning has been widely used in higher education as it provides better access to learning resources online, utilising technology to enhance learning. Despite growing evidence claiming that e-learning is as effective as traditional means of learning, the evidence is still very limited. This protocol aims to measure the impact of e-learning as compared to traditional face-to-face learning, both measured and perceived, on health sciences education -- in terms of improving students'/health professionals' satisfaction, knowledge, skills, and behaviours and patient-related outcomes. We will conduct a systematic review and meta-analysis of both randomised controlled trials and non-randomised controlled trials. Major databases will be searched for studies, and will be reported in accordance with PRISMA. A thematic analysis will be conducted for the included studies. If sufficient data are available, the random-effects model for meta-analysis will be performed. The outcome of this study will provide a basis for developing the best methods of e-learning in health sciences education.