Background The coronavirus disease (COVID-19) began to spread in mid-December 2019 from Wuhan, China, to most provinces in China and over 200 other countries through an active travel network. Limited by the ability of the country or city to perform tests, the officially reported number of confirmed cases is expected to be much smaller than the true number of infected cases. Objective This study aims to develop a new susceptible-exposed-infected-confirmed-removed (SEICR) model for predicting the spreading progression of COVID-19 with consideration of intercity travel and the difference between the number of confirmed cases and actual infected cases, and to apply the model to provide a realistic prediction for the United States and Japan under different scenarios of active intervention. Methods The model introduces a new state variable corresponding to the actual number of infected cases, integrates intercity travel data to track the movement of exposed and infected individuals among cities, and allows different levels of active intervention to be considered so that a realistic prediction of the number of infected individuals can be performed. Moreover, the model generates future progression profiles for different levels of intervention by setting the parameters relative to the values found from the data fitting. Results By fitting the model with the data of the COVID-19 infection cases and the intercity travel data for Japan (January 15 to March 20, 2020) and the United States (February 20 to March 20, 2020), model parameters were found and then used to predict the pandemic progression in 47 regions of Japan and 50 states (plus a federal district) in the United States. The model revealed that, as of March 19, 2020, the number of infected individuals in Japan and the United States could be 20-fold and 5-fold as many as the number of confirmed cases, respectively. The results showed that, without tightening the implementation of active intervention, Japan and the United States will see about 6.55% and 18.2% of the population eventually infected, respectively, and with a drastic 10-fold elevated active intervention, the number of people eventually infected can be reduced by up to 95% in Japan and 70% in the United States. Conclusions The new SEICR model has revealed the effectiveness of active intervention for controlling the spread of COVID-19. Stepping up active intervention would be more effective for Japan, and raising the level of public vigilance in maintaining personal hygiene and social distancing is comparatively more important for the United States.