In rice cultivation, there are controversial reports on net impacts of nitrogen (N) fertilizers on methane (CH 4) emissions. Nitrogen fertilizers increase crop growth as well as alter CH 4 producing (Methanogens) and consuming (Methanotrophs) microbes, and thereby produce complex effects on CH 4 emissions. Objectives of this study were to determine net impact of N fertilizers on CH 4 emissions and to identify their underlying mechanisms in the rice soils. Database was obtained from 33 published papers that contained CH 4 emissions observations from N fertilizer (28–406 kg N ha−1) treatment and its control. Results have indicated that N fertilizers increased CH 4 emissions in 98 of 155 data pairs in rice soils. Response of CH 4 emissions per kg N fertilizer was significantly (P < 0.05) greater at < 140 kg N ha−1 than > 140 kg N ha−1 indicating that substrate switch from CH 4 to ammonia by Methanotrophs may not be a dominant mechanism for increased CH 4 emissions. On the contrary, decreased CH 4 emission in intermittent drainage by N fertilizers has suggested the stimulation of Methanotrophs in rice soils. Effects of N fertilizer stimulated Methanotrophs in reducing CH 4 emissions were modified by the continuous flood irrigation due to limitation of oxygen to Methanotrophs. Greater response of CH 4 emissions per kg N fertilizer in urea than ammonia sulfate probably indicated the interference of sulfate in the CH 4 production process. Overall, response of CH 4 emissions to N fertilizers was correlated with N-induced crop yield (r = +0.39; P < 0.01), probably due to increased carbon substrates for Methanogens. Using CH 4 emission observations, this meta-analysis has identified dominant microbial processes that control net effects of N fertilizers on CH 4 emissions in rice soils. Finally, we have provided a conceptual model that included microbial processes and controlling factors to predict effects of N fertilizers on CH 4 emissions in rice soils.