Introduction: Lean healthcare outcome is usually measured with multiple key performance metrics but there is a lack of tools that enabled efficiency assessment. This research aimed to assess the efficiency among lean public emergency departments (ED) through Slack-Based Measure Data Envelopment Analysis (SBM-DEA) and evaluate the impact of lean on the efficiency in public emergency departments. Methods: A retrospective observational study design using data on the number of support staff, number of doctors, number of discharge, arrival to consultant and length of stay. Efficiency scores of 20 Malaysian public EDs were computed using SBM-DEA modelling and compared between before and after lean implementation. Results: A total of 13 out of 20 public EDs exhibited improvement in arrival to consultant and length of stay upon lean implementation. However, only 9 out of the 13 public EDs have had an improvement in efficiency score. Conclusion: Lean healthcare demonstrated a positive impact on the efficiency level of some public EDs. The SBM-DEA model offers the benchmarking capability and slack elimination information that may complement the lean continuous improvement philosophy.