As the population is shrinking in many municipalities in Japan, one of its effects is the vacant house crisis. The rise of empty houses profoundly affects the city’s society and economy, e.g., property value reduction, increased crime rate, poor sanitation, and housing market stagnation. To better understand the mechanism of the vacant house crisis, the present study proposes to examine the determinants of housing vacancy spatial distribution with the case study of the city of Sapporo. The results highlight the severe vacant cluster in the central city, which would seem to link to the disequilibrium housing market rather than the urban decline. Regarding vacancy determinants, demographic features were the most influential factors, followed by housing and neighborhood characteristics. Specifically, the vacancy correlated strongly with a high density of single households, children, the elderly (in the center), and a high share of offices. The surplus in housing supply and the inelasticity in housing structures also affected the vacancy significantly. On the contrary, a high percentage of private property, household ownership, and the elderly (in suburban) would reduce the vacancy. For other facilities, clinics, parking, public transportation, and educational institutions had a medium effect on the vacancy. Finally, the influence factors varied, across city areas, in magnitude and direction. These outcomes would be helpful for decision-making to alleviate the rise of vacant houses and their effect on the urban area.