Even in coastal oceans where tidal currents are predominant, long-term mean currents are of great interest since they are responsible for the transport of materials over long timescales. Tides could significantly affect mean currents in long, narrow straits due to tide-topography interaction, but it is yet unclear how and to what extent tides control throughflows. Here, we focus on the throughflow in the Seto Inland Sea, Japan, which has enormous impacts on the marine environment while its long-term mean characteristics, even the flow direction, are not well described by observations. By using a state-of-the-art ocean model, we show that the simulated throughflow is eastward on annual average and its volume transport is considerably suppressed by tides. It is found that tides enhance mixing and induce time-mean eddies, and both work to reduce the throughflow. A westward throughflow was previously estimated based on an acoustic measurement. The discrepancy between this estimate and our result would be due to whether or not such eddies are taken into account. These findings imply that tides may also suppress the throughflow of the other straits around the world. Revealing such tidal effects may contribute to a better performance of oceanic and climate simulations.