Methane (CH4) and nitrous oxide (N2O) fluxes were measured from paddy–upland rotation (three years for soybean and three years for rice) with different soil fertility due to preceding compost application for four years (i.e., 3 kg FW m-2 year-1 of immature or mature compost application plots and a control plot without compost). Net greenhouse gas (GHG) balance was evaluated by integrating CH4 and N2O emissions and carbon dioxide (CO2) emissions calculated from a decline in soil carbon storage. N2O emissions from the soybean upland tended to be higher in the immature compost plot. CH4 emissions from the rice paddy increased every year and tended to be higher in the mature compost plot. Fifty-two to 68% of the increased soil carbon by preceding compost application was estimated to be lost during soybean cultivation. The major component of net GHG emission was CO2 (82–94%) and CH4 (72–84%) during the soybean and rice cultivations, respectively. Net GHG emissions during the soybean and rice cultivations were comparable. Consequently, the effects of compost application on the net GHG balance from the paddy–upland rotation should be carefully evaluated with regards to both advantages (initial input to the soil) and disadvantages (following increases in GHG).