Female plot managers in Sub-Saharan Africa often realize significantly lower crop yields than their male counterparts. Even for legumes, which are often referred to as ‘women’s crops’, yields are significantly lower. This study investigated the underlying causes of this gender yield gap in groundnut production. The analysis is based on survey data from 228 farm households from two groundnut growing regions in Uganda. We used the Blinder-Oaxaca model to decompose factors that contribute to this yield gap. Results show 63% and 44% gender yield gaps for improved and local varieties, respectively, with female plot managers realizing less than their male counterparts. Improved groundnut seeds increase female plot manager’s yields but not the yields of male plot managers. Male advantage and female disadvantage combined account for more than 70% of the yield gap in both improved and local groundnut variety production and exceed pure productivity differences. Labor use differences between female and male plot managers and variety types explain the observed yield gap. Interventions and policies that increase women’s access to productive inputs including improved seed will significantly contribute to closing the yield gap, and thereby increase crop production, food security, as well as women’s incomes.