The study evaluates the gendered impacts of Agricultural Innovation Systems driven research on livelihood improvements in Africa. Using a case study from Malawi, the study employs a quasi-experimental research design with propensity score matching to establish a counterfactual and single differencing to measure impact. Results demonstrate that innovation systems driven agricultural research programs impact positively and significantly upon the livelihood outcomes of rural women. However there are differences in benefits accruing to women in rural communities depending on headship of the household with female-headed households benefiting more as compared to women in male-headed households. Policy implications are that; although innovation systems thinking has the potential to improve the livelihood outcomes of the poor in Africa; there is need for deliberate gender facilitation in program implementation to ensure equitable and sustainable livelihood improvements. This requires budgetary support to and capacity building of grassroots agricultural advisory service providers and researchers.