Track and preventive maintenance are necessary for the safe and comfortable operation of railways. Track displacement measured by track inspection vehicles or trolleys has been primarily used for track management. Thus, vibration data measured in in-service vehicles have not been extensively used for track management. In this study, we propose a new technique for estimating track irregularities from measured car body vibration for track management. The correlation between track irregularity and car body vibration was analysed using a multibody dynamics simulation of travelling rail vehicles. Gaussian process regression (GPR) was applied to the track irregularity and car body vibration data obtained from the simulation, and a method was proposed to estimate the track irregularities from the constructed regression model. The longitudinal-level, alignment, and cross-level irregularities were estimated from the measured car body vibrations and travelling speeds on a regional railway, and the results were compared with the actual track irregularity data. The results showed that the proposed method is applicable for track irregularity management in regional railways.