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Climate change is a major cause of changes in alpine and polar vegetation, particularly at the edges of distributions. In temperate regions, these changes are expected to occur at the timberline of alpine zones. On Mt. Fuji, the highest mountain in Japan, the timberline is located 2400–2500 m above sea level. Over a 40-year period (1978–2018), we researched changes in the timberline vegetation of Mt. Fuji. A permanent belt transect extending from the upper timberline to subalpine zones was set up in August 1978. Tree diameters and heights were recorded at the establishment of the transect and every 20 years afterwards. Over the 40 years of the study, the timberline advanced rapidly upwards, and the degree of vegetation cover above the timberline increased remarkably. Notably, the expansion of <i>Salix reinii</i> into the upper part of the timberline facilitated the subsequent spread of <i>Larix kaempferi</i> into this zone. Seedlings of <i>L. kaempferi</i> were particularly abundant at the upper timberline and became established on the uppermost part of the slope. The shape of <i>L. kaempferi</i> at the upper timberline changed from a prostrate form to an upright tree form. We conclude that the upward advance of the alpine timberline observed on Mt. Fuji is due to climate change.