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Combination of a pre-season wet soil condition and rice straw incorporation just before transplanting, which is typical for a tropical rice double cropping, can induce a flash of methane (CH4) emission shortly after the transplanting. The conventional practice of alternate wetting and drying (AWD) irrigation technique that typically starts at 21 days after transplanting (DAT) can hardly reduce this emission because the soil become methanogenic before the onset of AWD treatment. Field experiments were conducted in Central Luzon, Philippines, during the 2014-2017 dry rice seasons to examine the effects of the timing of rice straw/stubble incorporation on the efficacy of AWD in reducing the CH4 emission. Two treatments of the timing of stubble incorporation were stubbles incorporated during the start of wet land preparation (S1) and stubbles incorporated during the dry fallow tillage (S2). For the water management, we compared two treatments: continuous flooding (CF) and AWD with - 15 cm threshold for irrigation. The AWD under S2 was implemented earlier at 10 DAT. We observed a significant interaction (p < 0.01) between effects of AWD and straw management on CH4 emissions; the seasonal total CH4 emission was reduced by AWD compared with CF by 73% under S2, while the reduction was <20% under S1. The AWD significantly (p < 0.05) increased the nitrous oxide (N2O) emissions by 47 and 48% relative to CF under S1 and S2, respectively. The global warming potential (GWP, CH4 + N2O) and yield-scaled GWP were still substantially lower by 62 and 59%, respectively, in AWD than in CF under S2, but the reduction was not realized under S1 due to the relatively smaller CH4 reduction and increased N2O emission. The results confirm that pre-season aerobic stubble decomposition and earlier implementation of AWD enhanced AWD's mitigation potential in reducing substantially the CH4 emission from the tropical rice double-cropping system.