This paper presents a Bootstrap Super-DEA approach to evaluate route-level transit operational efficiency. Different from previous studies, the proposed model integrates the Bootstrap method with the super-DEA model, featuring the utilization of empirical data and repeated sampling to improve the estimation of the critical value precision statistics and to fine-tune the super-DEA efficiency derived from small sample dataset. To prevent the errors due to imperfect data and judgment mistakes, the proposed model also yields the interval-based estimation of efficiencies for each transit route operation. The proposed model has been successfully applied to evaluating the efficiencies of 17 bus routes in Chongqing City, China.