Introduction Emergency department overcrowding plagues departments worldwide with grave implications on patient comfort and care quality. Many standard approaches have been introduced without widespread success. A new approach is required. Focused Operations Management (FM) integrates novel managerial theories and practical tools into a systematic approach to complex systems, promoting insight and improving performance. It has allowed systems in the industry and service sectors to radically improve throughput and quality with no or little additional cost. The implementation of the FM in the emergency department setting to alleviate overcrowding has never been attempted, and it could revolutionize emergency department operations management. Methods Emergency department patient flow data affecting factors and outcomes from a large tertiary medical center, exclusively utilizing electronic patient records, will be collected. Root causes and influencing variables of emergency department overcrowding will be mapped and analyzed using FM tools. Later, alleviating measures will be developed and evaluated. During phase two, data will be collected from two additional emergency departments, measuring the impact of implementation of FM operational changes on emergency department flow parameters such as length of stay, wait times, clinical outcomes, and patient and staff satisfaction. Results Data collection and analysis of phase one of the study will be completed by March 2011 and presented at the conference. The authors speculate that the FM tools will allow better understanding of the root causes and affecting variables of emergency department overcrowding and help plan and later implement efficient interventions. Discussion The implementation of the novel management strategies of FM has revolutionized operations in many industries and services, helping them to drastically improve performance. The emergency department is a perfect candidate for the use of these tools, due to the overwhelming current operational difficulties (with overcrowding as a prominent symptom) and its complex high volume and high acuity patient flow.