This study analyzed the net carbon dioxide (CO2) emission reductions between 2005 and 2050 by using wood for energy under various scenarios of forest management and energy conversion technology in Japan, considering both CO2 emission reductions from replacement of fossil fuels and changes in carbon storage in forests. According to our model, wood production for energy results in a significant reduction of carbon storage levels in forests (by 46% to 77% in 2050 from the 2005 level). Thus, the net CO2 emission reduction when wood is used for energy becomes drastically smaller. Conventional tree production for energy increases net CO2 emissions relative to preserving forests, but fast-growing tree production may reduce net CO2 emissions more than preserving forests does. When wood from fast-growing trees is used to generate electricity with gas turbines, displacing natural gas, the net CO2 emission reduction from the combination of fast-growing trees and electricity generation with gas turbines is about 58% of the CO2 emission reduction from electricity generation from gas turbines alone in 2050, and an energy conversion efficiency of around 20% or more is required to obtain net reductions over the entire period until 2050. When wood is used to produce bioethanol, displacing gasoline, net reductions are realized after 2030, provided that heat energy is recovered from residues from ethanol production. These results show the importance of considering the change in carbon storage when estimating the net CO2 emission reduction effect of the wood use for energy.