Applications of automatic fare collection data were investigated, with a focus on analysis of travel time reliability and estimation of passenger route choice behavior. Beijing Metro was used as a case study. A rail journey was decomposed, and each component was studied with regard to the uncertainties involved. Methods were then designed and validated to infer platform elapsed time (PET) for through stations and platform elapsed time–transfer (PET-Trans) for transfer stations by using smart card transactional data, train schedules, and complementary manual surveys. With this information, the journey time distribution of any path can be established, and methods were proposed for inferring route choice proportions. After data preparation, the methods were applied to two typical origins and destinations from the Beijing Metro. Key values concerning travel time reliability, such as PET, PET-Trans, travelers left behind (unable to board), and path coefficients, were obtained and interpreted in detail. The outcome of this research could facilitate analysis of transit service reliability and passenger flow assignment in daily operations.