Forest therapy bases are essential ecological recreational locations to promote mental and physical health while at the same time allowing people to enjoy and appreciate the forest. The article took Japan, where the development of forest therapy is in a mature stage, as the research object. Using multi-data and the methodologies of Kernel Density Analysis in ArcGIS and GeoDetector, the spatial distribution characteristics of Japan’s forest therapy bases were investigated, as well as the influencing factors. The results reveal that the spatial distribution of forest therapy bases in Japan is unbalanced, with an aggregated distribution in economically developed and densely populated areas. The spatial density of natural landscape resources, Gross Domestic Product (GDP), the spatial density of population, distance from three major metropolitan areas, rail transit ridership, and spatial density of tourism resources are factors influencing the distribution of forest therapy bases in Japan. The factors interact with each other, forming the spatial distribution pattern. Among these factors, GDP has the greatest explanatory power for the spatial distribution of forest therapy bases in Japan, followed by the distance from Japan’s three major metropolitan areas and spatial density of tourism resources, while the spatial density of population, spatial density of natural landscape resources, and rail transit ridership have a relatively weaker influence on forest therapy bases in Japan. The findings provide some insight into the macroscopic layout of forest therapy bases in various regions of different countries, demonstrating that excellent transportation facilities and good natural resources are the fundamental considerations for the location of forest therapy bases and that densely populated urban areas with a strong economic foundation are key areas for the development of forest therapy bases. Additionally, to take advantage of industrial agglomeration and synergize regional development, considerations for merging with existing resources, such as national parks, forest parks, and recreation forests, should be made.