This paper combines nationally representative farm household data with geospatial climate data to investigate existing climate change effects on the gender agricultural productivity gap among male and female plot managers in Mali. In this study, the standardized precipitation index (SPI) and aridity index (Arindex) are computed as weather and climatic variables affecting the gender agricultural productivity gap. The Oaxaca-Blinder approach is applied to quantify the magnitude of the gender productivity gap due to climate change as well as the climatic variables that influence the gap at the mean and at the different quantiles. Findings show that female structural disadvantage is largely driven by climate change. Recentered influence function decomposition results further indicate that higher-than-normal precipitation that predominated in the semi-arid region during the last decade contributes significantly to widening the gender agricultural productivity gap along the percentile distribution. The two first percentiles of the aridity index from the male structural effect also contribute to enlarging the gap. Overall, climate change is found to be one of the major factors of gender disparity along the productivity distribution. The results imply that special attention should be given to gender inclusion in smart climate change adaptation and mitigation strategies.