The transport sector is a major contributor to anthropogenic climate change through the emissions of large amounts of greenhouse gases from fossil fuel combustion. Private vehicles account for almost half of the transport energy demand, and are thus a major target for climate change mitigation efforts. However, emissions from private vehicles can have large variability due to various geographic, demographic and socioeconomic factors. This study aims to understand how such factors affect private vehicle emissions in Japan using a nationally representative survey of household energy consumption (n = 7370) for 2017. The results indicate a large temporal and spatial variability in private vehicle emissions. Annual emissions show three peaks associated with major holiday seasons in winter and summer. Some of the more noteworthy spatial patterns are the higher emissions in prefectures characterized by low population density and mountainous terrain. Income, city size and the fuel-saving driving behavior all have a significant effect on emissions. The results indicate the need for sub-regional and socioeconomically-sensitive mitigation efforts that reflect the very different emission patterns, and the factors affecting them. The strong effect of city size, which is often much more clear-cut than between prefectures, suggests that it is more appropriate to approach transport decarbonization in Japan at the city level.