In this paper, a vibration-based system identification to estimate the relative prestress force effects on the structural parameters of prestressed concrete (PSC) girder is performed. Firstly, vibration tests are performed on a lab-scaled PSC girder for which modal parameter was measured for several prestress-force cases. Secondly, the numerical modal analysis is performed by using initial finite element (FE) model from geometric, material and boundary condition of the lab-scaled PSC girder. Thirdly, the vibration-based system identification is performed to update FE model by identifying structural parameter compared with experimental results. Finally, the prestress force effects on the structural parameters is estimated from the analysis on the relationship between prestress forces and the relative changes in the structural parameters.