The Japanese squirrel's native range includes large portions of the islands of Honshū, Shikoku, and Kyūshū.

The Japanese squirrel is absent from Hokkaido, where it is replaced by the related red squirrel (Sciurus vulgaris), which is conversely absent from the rest of the Japanese archipelago outside Hokkaido.

Recently, populations in south-western Honshū and Shikoku decreased, and those on Kyūshū disappeared.

One of the factors affecting the recent local extirpations of this species seems to be forest fragmentation by humans.

This strategy seems to be efficient since it minimizes the time to finish eating an entire walnut.