Tidal currents have two types of intrinsic long-term fluctuations. The one is single tidal constituent such as Ssa and the other one is interferences between tidal constituents. The effect of the long-term fluctuation of tides on the resource assessment for tidal current energy generation system near Japan has been described based on the predictions using data-assimilative global barotropic tide model results. It is shown that monthly mean tidal energy flux varies by more than 20% over a year in the most of the prospective areas. The result indicates the intrinsic long-term fluctuations need to be considered in the resource assessment of tidal current power generation system.