The effects of biochar (BC) on methane (CH4) emission may vary with nitrogen (N) fertilization rate, organic inputs, and water management. In this short review, we studied the changes in the direction and magnitude of CH4 emission by BC under these different conditions. Literature data indicated that co-application of BC with N fertilizer may increase or decrease CH4 emission depending on the N fertilization rates. Although the threshold N fertilization rate for the enhanced CH4 emission by BC is unclear, it was suggested that N fertilization may enhance BC-induced CH4 oxidation via the supply of N to methanotrophs. Although organic inputs stimulate CH4 emission, co-application of BC with organic inputs efficiently decreases CH4 emission by reducing C substrate availability for methanogens via sorption onto BC particles. The application of BC also enhances CH4 oxidation under water-saving irrigation to stimulate the methanotroph activity under aerobic conditions. Our study suggests that application of BC may be a measure to mitigate CH4 emission from paddy soils amended with organic inputs and it may further enhance CH4 oxidation under water-saving irrigation.