Across the globe, increasing populations of Cervidae have the potential to modify ecosystems. Long-term grazing pressure by deer not only alters vegetation but also affects ecosystem functions and interspecific interactions. It is recognized as a significant factor in ecological degradation. Alpine vegetation (i.e., alpine meadow) is an icon of alpine ecosystems and has thrived for centuries without the presence of large herbivores in Japan. However, in the alpine zone (> 2700 m a.s.l.) of the South Alps National Park in central Honshu, Japan, sika deer (Cervus nippon) were first seen in the 1990s; thereafter, the vegetation noticeably changed starting in the 2000s. Nonetheless, virtually no information exists on habitat selection by these alpine sika deer. Here we analyzed (1) the altitudinal movement patterns of alpine sika deer, (2) the significant environmental factors affecting their habitat selection, and (3) estimated the relative probability of their habitat use via resource selection functions (RSF). The mean altitudinal difference between summer and winter home ranges was 1186 m, and the alpine sika deer arrived at the alpine ridgeline in June when the snow cover at > 2400 m a.s.l. rapidly decreased. The mean altitude in the summer home range was 2635 +/- 135 m. Alpine meadow, followed by Betula forests and tall grasslands, were preferred habitats by deer. The deer also preferred areas where snow melted in late spring and early summer. The deer's core habitat, indicated by higher RSF values (>= 0.65), covered 45.2% of the study area, mostly distributed in the alpine zone. Our estimates clearly suggest the urgent need to prioritize specific areas for the conservation of the alpine vegetation in the South Alps National Park in Japan.