BACKGROUND: Over the past two decades, Uganda has experienced a significant increase in clinical research driven by both academia and industry. This has been combined with a broader spectrum of research proposals, with respect to methodologies and types of intervention that need evaluation by Research Ethics Committees (RECs) with associated increased requirement for expertise. We assessed the competencies of REC members regarding review of research protocols with complex and emerging research study designs. The aim was to guide development of a training curriculum to improve the quality of scientific and ethical review. METHODS: This was a cross-sectional study design, with quantitative data collection methods. Research Ethics Committee members completed a structured pre-coded questionnaire on current competence with complex and emerging study design. REC members were asked to outline a list of additional topics for which they needed training. Data from coded questions were entered into Epidata Version 3.1 and then exported to STATA Version14.1 for analysis. Descriptive analysis was performed and findings are presented using percentages and frequencies. RESULTS: We enrolled 55 REC members from 6 RECs who have a total of 97 members. The majority of whom were males (56.4%, n = 31/55). The level of competence for review of selected study design was lowest for Controlled Human Infection Model (10.9%, n = 6) and reverse pharmacology design (10.9%, n = 6), and highest for cluster randomized study design (52.7%, n = 29) and implementation science research (52.7%, n = 29). CONCLUSION: Competence for review of research protocols with complex and emerging study design was low among participating REC members. We recommend prioritising training of REC members on complex and emerging study designs to enhance quality of research protocol review.