Between August and October 2015, we found five carcasses of the wild Malayan flying lemurs (Galeopterus variegatus) in the Pangandaran Nature Reserve in West Java, Indonesia. Such short-term mortality events have never been reported for this species. In order to address the potential factors causing it, we firstly compared the estimated population density of the flying lemurs before and after the mortality events. Secondary we collected data on temperature, monthly rainfall, and food availability (in terms of phenology scores), from which we extracted unique feature(s) when the mortality events occurred. Mean (± SD) population size within the study site (38 ha) was 27 ± 24, and the five carcasses accounted for 10–20% of the population. The availability of young leaves, monthly rainfall, and maximum temperature were significantly lower during mortality events than in other years. The rainfall was the lowest in the past ten years. This suggests that drought accompanied by food scarcity likely causes the mortality. However, other potential underlying causes such as epidemics and the recent development of a resort near the study site cannot be ruled out. After the mortality events, the population size started to recover.