As a key axis of metropolitan public transport, exclusive median bus lanes (EMBLs) are facing operational limits owing to urban expansion and increased traffic demand, with queues at bus stops during peak hours causing severe delays. This study aims to empirically identify the phenomenon of queue-based delays at the stop level, that is difficult to explain using conventional capacity calculation methods, and to propose an operational strategy for its mitigation. By realistically assessing passenger inconvenience through a revised “additional passenger travel time” calculation based on bus travel, this study provides a balanced analysis of the tradeoff between system efficiency and passenger convenience, thereby contributing to the development of sustainable urban transit systems. This study compared current all-stop operations with two skip-stop scenarios in Songpa-daero, a major arterial corridor in Seoul. Using an actual bus management system and transit card data, key performance indicators including queue length, travel time, dwell time, and additional passenger travel time were analyzed. Scenario I applied an A/B service-style alternating stop operation, whereas Scenario II implemented a hybrid approach, designating hub stops at key locations. Simulation modeling was used to evaluate the system-wide impacts during peak hours. The analysis revealed that skip-stop operations had significant potential to improve EMBL performance; however, the benefits were subject to a trade-off with passenger inconvenience. Scenario I with alternating stops was most effective in reducing the queue length and overall travel time. However, it also resulted in the largest increase in additional passenger travel time calculated with the revised methodology. In contrast, Scenario II with hub stops, while showing slightly less improvement in operational efficiency, presented a more balanced outcome by mitigating the burden of additional travel time for passengers through hub stops, thereby enhancing service equity. Both scenarios showed reduced dwell times at most stops, indicating the alleviation of boarding and alighting congestion. This study confirmed that skip-stop strategies could effectively improve the operational efficiency of EMBLs by reducing queue lengths and travel times. However, the additional passenger travel time, including bus transfers, is a critical factor that must be considered. Scenario I was evaluated as superior for maximizing the operational efficiency, whereas Scenario II was a better alternative for securing a balance with passenger convenience. This study is significant because it presents an analytical framework for quantifying queue-based delays and realistically assessing passenger impact. Although limitations remain, such as not fully capturing the complex decision-making processes of actual passengers, the methodology and findings offer practical guidance for urban transport planners seeking data-driven solutions to EMBL congestion, emphasizing the importance of the passenger perspective in skip-stop strategy design.