Vortex-induced vibration (VIV) of long-span bridges can be of large amplitude, which can influence serviceability. Therefore, it is important to predict the response of vortex-induced vibration to aid the management of long-span bridges. A novel data-driven model is proposed to predict the time history of the dynamic response of VIV events. Specifically, the proposed model consists of gated recurrent unit (GRU) neural networks and the Newmark-beta method. GRU neural networks can perform accurate sequential prediction, and the Newmark-beta method can complement the physical meaning of the middle output of the proposed model. To aid the accurate prediction of the amplitude of VIV events, the proposed model employs weighted mean square error as the loss function, which can put more emphasis on the amplitude. The proposed model is validated on measured VIV events of a long-span suspension bridge. The weighted mean absolute percentage error and Pearson correlation coefficient of the trained model indicate the effectiveness of the proposed model.