In response to long-term operation of prestressed concrete railway bridges, the girder body will arch because of creep, which may influence the running stability of high-speed trains. Usually, the deformation of the rail-bridge system under the creep effect is calculated by a finite element model with the rail geometry deformation input as additional irregularity. The original irregularity is superimposed to the coupled system of the train and bridge to calculate the dynamic response of the system. However, such a strategy is time-consuming and cannot accurately integrate the uncertainty of the original rail irregularity. This paper presents an analytical formula for predicting the rail deformation caused by concrete creep. The rail deformation caused by the bridge upper arch can be quickly predicted by the creep amplitude of the bridge. The creep deformation of the rail is applied as an irregularity excitation to the train-track-bridge coupled system (TTBCS). In addition to creep irregularities, original random irregularities also exist on the track. The Karhunen-Loéve expansion method is adopted to represent the random track irregularity that considers creep deformation. The results achieve good agreement with the initial samples. Subsequently, the TTBCS model is established to analyze the dynamic responses of different train speeds and different bridge creep deformations using a stochastic dynamic analysis method. This method achieves very high agreement with the Monte Carlo method, and the error rate of the mean bridge displacement calculated by both methods under the same working conditions was only 0.0351%. Finally, the upper probability limit value of the creep of the bridge is put forward: at a speed of a high-speed train of 350 km/h, the creep upper arch limit is only 7 mm. These probability limits at different train speeds have guiding significance for the design, maintenance, and repair of the actual medium–high-speed railway concrete supported beam bridge.