Food nitrogen footprints (N-footprints) for China in 2013 and Japan in 2011 were estimated with a top-down method (the N-Input method). This method evaluates the new nitrogen input for food production in both the country of interest and the countries from which food is imported. The food N-footprints in China and Japan were 21.96 kg N capita^–1 yr^–1 and 18.44 kg N capita^–1 yr^–1, respectively, which were similar to published values estimated with the N-calculator method, which evaluates nitrogen loss to the environment during production and consumption. To compare the nitrogen use efficiency for different type of food supplied in both countries, we calculated the ratio (R _I/O) of new nitrogen input to nitrogen output to each type of food domestically produced and imported. R _I/O for crops tended to be larger in China than in Japan, whereas the opposite was observed for livestock products. The larger N-footprint in China was mainly attributable to the higher per capita protein intake in China compared with Japan; per capita nitrogen intake in China has been increasing and is 6.95 kg N yr^–1 in 2013, exceeding the intake in Japan (5.86 kg N yr^–1 in 2011). We also showed that R _I/O can be converted to the virtual nitrogen factors, which can be used for N-calculator method, in heavy food importing countries. Some methodological differences in food N-footprint estimation methods were discussed. For example, approximately 10% of the N-footprint in both countries by the N-Input method was attributable to supply of secondary products such as sugar, vegetable oil and alcoholic beverages, but these were not included in the N-calculator method.