Women comprise 50% of the agricultural labor force in Sub-Saharan Africa, but manage plots that are reportedly on average 20–30% less productive. As a source of income inequality and aggregate productivity loss, the country-specific magnitude and drivers of this gender gap are of great interest. Using national data from the Uganda National Panel Survey for 2009–10 and 2010–11 that include a full agricultural module and plot-level gender indicator, the gap before controlling for endowments was estimated to be 17.5%. Panel data methods were combined with an Oaxaca decomposition to investigate the gender differences in resource endowment and return to endowment driving this gap. Although men have greater access to inputs, input use is so low and inverse returns to plot size so strong in Uganda that smaller female-managed plots have a net endowment advantage of 12.9%, revealing a larger unexplained difference in return to endowments of 30.4%. One-half of this is attributed to differential returns to the child dependency ratio, implying that greater child care responsibility is the largest driver of the gap. Smaller drivers include differential uptake of cash crops, differential uptake and return to improved seeds and pesticides, and differential returns to male-owned assets.