The rice cyst nematode, Heterodera elachista, previously reported only in Japan, has recently been detected elsewhere in Asia and in Europe. Because control of H. elachista by fumigation is economically impractical, control through farming practices in the form of tillage, cover cropping, and N fertilization is needed. We evaluated the effects of three tillage systems (moldboard plow [MP] with rotary cultivation, rotary cultivator [RC], and no-tillage [NT]), three winter alternatives (fallow; rye or hairy vetch cover crops), and two rates of N fertilization (0 and 100kgha −1 on upland rice and 0 and 20kgha −1 on soybean) on population densities of H. elachista in 2003 to 2011. During the first 3 years of continuous upland rice cropping, population densities were very low. By 4 years (2006), they increased markedly in MP and RC (216.0 and 282.8 nematodes, respectively, per 100g dry soil) but not in NT (111.1 per 100g). However, by 5 years, they increased markedly in NT too, eliminating any differences between tillage systems. After conversion to soybean, H. elachista densities decreased in all treatments, but decreased fastest in NT. Cover cropping and N fertilization did not markedly affect H. elachista densities, but cover cropping reduced the proportion of H. elachista among all nematodes in one year, and N fertilization increased the degree of rice yield reduction by increasing H. elachista abundance by the 5th year. Our results suggest that NT and crop rotation can help in controlling H. elachista densities.