Human ageing and population decline in Japan are causing agricultural field abandonment and providing new habitats for Japanese sika deer and wild boar. These species have expanded their distribution and increased in abundance across Japan and are causing increased agricultural damage. Effective countermeasures must factor in the behavioural flexibility of sika deer and wild boar. The aim of this study was to examine the effects of hunting and indirect human activities on the activity patterns of sika deer in central Japan and compare these with previous findings on wild boar. Camera traps were used to observe activity patterns of both species and that of humans. Sika deer and wild boar were most active at night during the non-hunting season. Hunting activities significantly reduced sika deer and wild boar activity patterns. In the non-hunting season, nocturnal activity of sika deer increased with decreasing distance to settlement. A similar, but weak response was also observed for wild boar. This study suggests that sika deer and wild boar avoid humans and human-dominated areas by being nocturnal. The recent introduction of night hunting might help to control wildlife populations, but monitoring will be necessary to confirm this expectation.