Many bird species with heterogeneous distribution are at risk of extinction. It is essential to identify and elucidate environmental factors explaining such distribution patterns to develop effective conservation strategies for those species. Yellow Bunting Emberiza sulphurata is an endangered migrant bird species exhibiting heterogeneous breeding distribution in Japan. Here we clarify the spatial distribution and the altitudinal range of the Yellow Bunting breeding range, and detect environmental factors (e.g., climate and topography) influencing their distribution pattern using an extensive dataset from the national breeding birds survey of Japan. The presence of Yellow Bunting during the breeding season (1997–2002) and six environmental factors (temperature, snow depth, elevation, tertiary layer, landslide area and forest edge density) were analyzed using maximum entropy models (MaxEnt). We found that Yellow Buntings were present in a higher proportion of survey grids in northern Honshu (the main island of Japan) than elsewhere in the country, and they mainly occurred in areas below 700 m above sea level. Moreover, the elevation of the occupied grids decreased with latitude. Temperature and snow depth were of greater importance (0.380 and 0.350, respectively) than other factors in explaining the breeding distribution of the Yellow Bunting. Our study highlighted the location of the core areas of the Yellow Bunting's breeding distribution, and demonstrated that lower temperature and deeper snow cover are the critical determinants of those areas. There may be abundant prey and fewer avian competitors, such as resident bird species, in colder regions, and more frequent snow avalanches and water from melting snow may establish the marshy and bushy habitat preferred by Yellow Buntings. These findings are essential for developing effective conservation strategies for the endangered Yellow Bunting. As past mass-trapping may have also influenced the heterogeneous distribution of the Yellow Bunting, this is an important avenue for future research from a different perspective.