As the basic unit of railway transportation service, railway operation enterprises have receive1d more and more attention. The improvement of transportation efficiency of railway operation enterprises plays a vital role in developing railway transportation. We used the three-stage DEA-Bootstrap model to calculate the transportation efficiency of 38 railway operators worldwide from 2000 to 2020. Compared with the traditional DEA model and the three-stage DEA model, the three-stage DEA-Bootstrap not only eliminates the influence of environmental variables on the efficiency value, but also revises the influence of random factors on the efficiency, and obtains the efficiency closest to the real value. The results show that China Railways (CR), Japan Railways (JR), India Railways (IR), and Russian Railways (RZD) all have high-efficiency rankings in the first stage, the third stage, after Bootstrap correction. Railway comprehensive efficiency is mainly composed of scale efficiency and technical efficiency. And scale efficiency (SE) is the most important factor that determines the overall efficiency of an enterprise. Companies with high-scale efficiency tend to rank relatively high in overall efficiency. Based on the revised characteristics of pure technical efficiency and scale efficiency, we divided the sample enterprises into regions and proposed a promotion strategy relying on the characteristics of regional development. This study would promote improving the transportation efficiency of railway operating enterprises and developing the entire railway transportation industry.