As the influence of climate change on tropical forests becomes apparent, more studies are needed to understand how changes in climatic variables like rainfall are likely to affect tree phenology. Using a twelve-year dataset (2005–2016), we studied the impact of seasonal rainfall patterns on the fruiting phenology of 69 tree species in the rain forest of southeastern Madagascar. We found that average annual rainfall in this region has increased by >800mm (23%) during this period relative to that recorded for the previous 40 years, and was highly variable both within and between years. Higher monthly measures of fruiting richness and the intensity of fruiting in our sample community were significantly associated with higher levels of rainfall. We also found that less rainfall during the dry season, but not the wet season, was associated with a significant shift toward later timing of peak richness and peak intensity of fruiting in the subsequent 12 months; however, this pattern was driven primarily by an extreme drought event that occurred during the study period. Longer time scales of phenology data should be examined in the future to see if this pattern holds. Madagascar is expected to experience more extremes in rainfall and drought with increasing climate change. Thus, understanding the impacts of variable precipitation on the timing of reproduction of forest trees will have important consequences for plant reproduction and the ability of Madagascar’s wildlife to cope with a changing climate.