AbstractE-learning has been widely used in higher education as it provides better access to learning resources online, utilising technology – regardless of learners’ geographical locations and timescale – to enhance learning. Despite growing evidence claiming that e-learning is as effective as traditional means of learning, there is very limited evidence. This protocol aims to assess the effects of e-learning factors that impact on health sciences education (HSE). We will conduct a systematic review meta-analysis research of both randomised controlled trials and non-randomised controlled trials. Seven databases – MEDLINE, EMBASE, Allied & Complementary Medicine, DH-DATA, PsycINFO, CINAHL, and Global Health – will be searched, from 1980 through 2020. The PRISMA-P checklist will be used while preparing this protocol. Two reviewers will independently screen the papers and extract data. We will utilise the JBI quality appraisal tools for quantitative and qualitative studies, and Mixed Methods Appraisal Tool appraisal tools to assess the quality. A narrative synthesis, using thematic analysis, will be conducted for the included studies. If sufficient data are available, the random-effects model for meta-analysis will be performed to measure the effect size of e-learning on health sciences education or the strengths of relationships. The outcome of this review will provide a useful checklist of potential factors to develop an e-learning approach in HSE. This might provide a basis for developing the best methods of e-learning in education so that e-learning policy in education and learning settings in the HSE context could be administered effectively, efficiently and equitably.