Predicting how species respond to changes in climate is critical to conserving biodiversity. Modeling efforts to date have largely centered on predicting the effects of warming temperatures on temperate species phenology. In and near the tropics, the effects of a warming planet on species phenology are more likely to be driven by changes in the seasonal precipitation cycle rather than temperature. To demonstrate the importance of considering precipitation-driven phenology in ecological studies, we present a case study wherein we construct a mechanistic population model for a rare subtropical butterfly (Miami blue butterfly, Cyclargus thomasi bethunebakeri) and use a suite of global climate models to project butterfly populations into the future. Across all iterations of the model, the trajectory of Miami blue populations is uncertain. We identify both biological uncertainty (unknown diapause survival rate) and climate uncertainty (ambiguity in the sign of precipitation change across climate models), and their interaction as key factors that determine persistence vs. extinction. Despite uncertainty, the most optimistic iteration of the model predicts that Miami blue butterfly populations will decline under the higher emissions scenario (RCP 8.5). The lack of climate model agreement across the projection ensemble suggests that investigations into the effect of climate change on precipitation-driven phenology require a higher level of rigor in the uncertainty analysis compared to analogous studies of temperature. For tropical species, a mechanistic approach that incorporates both biological and climate uncertainty is the best path forward to understand the effect shifting precipitation regimes have on phenology and population dynamics.