Subway stations have been proliferating underneath cosmopolitan metropolises with subway lines forming complex webs connected in strategic transfer stations. The efficiency of the subway system thus heavily weighs on the efficiency at these transfer stations. However, few studies have been conducted on transfer efficiency at transfer stations due to the complexities involved. As the first study of its kind in the subway context, we analyze the transfer efficiency of the subway transfer stations in Seoul, one of the megacities in the world, and demonstrate how transfer efficiency can be analyzed using bootstrap-based DEA technique. Based on the results, we discuss the reasons behind the inefficiency of subway transfer stations and possible ways to improve them into efficient decision-making units.