Existing gender inequality is believed to be heightened as a result of weather events and climate-related disasters that are likely to become more common in the future. We show that an already marginalized group—female-headed households in South Africa—is differentially affected by relatively modest levels of variation in rainfall, which households experience on a year-to-year basis. Data from three waves of the National Income Dynamics Survey in South Africa allow us to follow incomes of 4,162 households from 2006 to 2012. By observing how household income is affected by variation in rainfall relative to what is normally experienced during the rainy season in each district, our study employs a series of naturally occurring experiments that allow us to identify causal effects. We find that households where a single head can be identified based on residency or work status are more vulnerable to climate variability than households headed by two adults. Single male-headed households are more vulnerable because of lower initial earnings and, to a lesser extent, other household characteristics that contribute to economic disadvantages. However, this can only explain some of the differential vulnerability of female-headed households. This suggests that there are traits specific to female-headed households, such as limited access to protective social networks or other coping strategies, which makes this an important dimension of marginalization to consider for further research and policy in South Africa and other national contexts. Households headed by widows, never-married women, and women with a non-resident spouse (e.g., “left-behind” migrant households) are particularly vulnerable. We find vulnerable households only in districts where rainfall has a large effect on agricultural yields, and female-headed households remain vulnerable when accounting for dynamic impacts of rainfall on income.