Abstract Background: Emergency department (ED) overcrowding has become a significant problem throughout the large medical centers, leading to possible threatened medical quality, causing raised stress levels among staff and patients in EDs, and most importantly, adversely affecting patient outcomes. Due to its complexity, a large concerted group effort will be needed to increase awareness, implement proposed solutions, and make a change. ED overcrowding is a multifaceted problem that will require a multifaceted solution. Methods: We set up the "Input-Throughput-Output" model provides a structure for examining the factors that affect ED access, quality and outcomes. Using this model, we clarify the issues of ED overcrowding into three stages, propose ways to obtain needed information in each stage, test the strategies and then evaluate their outcomes. We utilized the analytic hierarchy process (APH) method to measure the weights of the physician¡¦s stress and arrange more efficacious and flexible duties accordingly. Results: This is a prospective study investigating ED overcrowding at this medical center from January 2008 through December 2009. Hospitals developed and implemented a number of best practices revolved around patient flow initiatives, specifically looking to improve input, throughput, and output. Conclusion: This study suggests that a decrease in ED overcrowding can be achieved through ongoing collaboration of the indicators and the implementation of best practices via the Input-Throughput-Output model.