We measured nitrous oxide (N2O) and carbon dioxide (CO2) fluxes from the soil surface and in the soil through to a depth of 0.3 m, and their concentration profiles through to a depth of 0.6 m in both a Gray Lowland soil with macropores and cracks and an Andosol with undeveloped soil structure in central Hokkaido, Japan. The objective of the present study was to elucidate any differences in N2O production and flux in the soil profile between these two soil types. In the Gray Lowland soil, the N2O concentration above 0.4 m increased with an increase in soil depth. In the Andosol, there were no distinctive N2O concentration gradients in the topsoil when the N2O flux did not increase. However, the N2O concentration at a depth of 0.1 m significantly increased and this concentration was higher than the concentration below 0.2 m when the N2O flux greatly increased. Thus, the N2O concentration profiles were different between these two soils. The contribution ratios of the N2O produced in the top soil (0–0.3 m depth) to the total N2O emitted from the soil to the atmosphere in the Gray Lowland soil and the Andosol were 0.86 and 1.00, respectively, indicating that the N2O emitted from the soil to the atmosphere was mainly produced in the top soil. However, the contribution ratio of the subsoil to the N2O emitted from the Gray Lowland soil was higher than that of the Andosol. There was a significant positive correlation between the N2O flux through to a 0.3 m depth and the flux from the soil to the atmosphere in the Gray Lowland soil only. These results suggest that N2O production in the subsoil of the Gray Lowland soil could have been activated by NO3− leaching through macropores and cracks, and subsequently the N2O produced in the subsoil could have been rapidly emitted to the atmosphere through the macropores and cracks.