Train-induced vibration exhibits a potential dynamic impact on historic buildings and especially on those with high historical and cultural value. Under the long-term reciprocating load of train vibrations, structural fatigue damage can occur, and thus, a significant problem involves effectively evaluating and mitigating vibration impact on historic buildings while developing a rail transit system. In the present study, train-induced vibration impact and dynamic behavior of Probhutaratna pagoda in the suburb of Beijing, which has a history of approximately 1000 years, was investigated. To examine the dynamic behavior of the Probhutaratna pagoda and determine the weakest position in its architectural damage under train loads, its dynamic characteristics were measured. The free vibration modes were identified based on the dynamic measurement results. Subsequently, a finite element (FE) model of the Probhutaratna pagoda was constructed and the models and train-induced structural responses were compared with measured results. Finally, the structural dynamic responses to moving train loads were analyzed in detail. The results indicate the following conclusions. (1) The dominant frequency of the ambient vibration is below 4 Hz, and the dominant frequency of the train-induced vibration is between 8 and 16 Hz. (2) The first, second, and third order natural frequencies are 1, 3.25, and 6 Hz, respectively, in the west–east direction, and are 1, 3.25, and 6.25 Hz, respectively, in the north–south direction. (3) The two weakest locations (A and B) of the Probhutaratna pagoda are observed at the spire bottom and west gate of the first floor. At location A, the maximum principal stress reached 243.6 N/m2 and the corresponding maximum tensile strain reached 3.74×10-7.