Accurate predictions of bus arrival times help passengers arrange their trips easily and flexibly and improve travel efficiency. Thus, it is important to manage and schedule the arrival times of buses for the efficient deployment of buses and to ease traffic congestion, which improves the service quality of the public transport system. However, due to many variables disturbing the scheduled transportation, accurate prediction is challenging. For accurate prediction of the arrival time of a bus, this research adopted a recurrent neural network (RNN). For the prediction, the variables affecting the bus arrival time were investigated from the data set containing the route, a driver, weather, and the schedule. Then, a stacked multilayer RNN model was created with the variables that were categorized into four groups. The RNN model with a separate multi-input and spatiotemporal sequence model was applied to the data of the arrival and leaving times of a bus from all of a Shandong Linyi bus route. The result of the model simulation revealed that the convolutional long short-term memory (ConvLSTM) model showed the highest accuracy among the tested models. The propagation of error and the number of prediction steps influenced the prediction accuracy.