Nitrous oxide (N2O) and methane (CH4) fluxes from a fertilized timothy (Phleum pratense L.) sward on the northern island of Japan were measured over 2 years using a randomized block design in the field. The objectives of the present study were to obtain annual N2O and CH4 emission rates and to elucidate the effect of the applied material (control [no nitrogen], anaerobically digested cattle slurry [ADCS] or chemical fertilizer [CF]) and the application season (autumn or spring) on the annual N2O emission, fertilizer-induced N2O emission factor (EF) and the annual CH4 absorption. Ammonium sulfate was applied to the CF plots at the same application rate of NH4-N to the ADCS plots. A three-way ANOVA was used to examine the significance of the factors (the applied material, the application season and the year). The ANOVA for the annual N2O emission rates showed a significant effect with regard to the applied material (P = 0.042). The annual N2O emission rate from the control plots (0.398 kg N2O-N ha−1 year−1) was significantly lower than that from the ADCS plots (0.708 kg N2O-N ha−1 year−1) and the CF plots (0.636 kg N2O-N ha−1 year−1). There was no significant difference in the annual N2O emission rate between the ADCS and CF plots. The ANOVA for the EFs showed insignificance of all factors (P > 0.05). The total mean ± standard error of the EFs (fertilizer-induced N2O-N emission/total applied N) was 0.0024 ± 0.0007 (kg N2O-N [kg N]−1), which is similar to the reported EF (0.0032 ± 0.0013) for well-drained uplands in Japan. The CH4 absorption rates differed significantly between years (P = 0.014). The CH4 absorption rate in the first year (3.28 kg CH4 ha−1 year−1) was higher than that in the second year (2.31 kg CH4 ha−1 year−1), probably as a result of lower precipitation in the first year. In conclusion, under the same application rate of NH4-N, differences in the applied materials (ADCS or CF) and the application season (autumn or spring) led to no significant differences in N2O emission, fertilizer-induced N2O EF and CH4 absorption.