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Livestock diseases are a major barrier to productivity for both male and female livestock keepers in Africa. In Kenya, two of the most devastating livestock diseases are Newcastle Disease (ND) in poultry and Contagious Caprine Pleuropneumonia (CCPP) in goats. Female livestock keepers tend to own more small ruminants (goats, sheep, etc.) and poultry and their livelihoods are adversely affected if their herds are not vaccinated against these diseases. Livestock farming has gender specific challenges and opportunities, with implications for the empowerment of women smallholder farmers, their household well-being, food security, and livelihoods. There is a need to estimate the level to which women benefit personally, socially, and economically from keeping livestock, yet there are very few studies that can measure if livestock production does in fact empower women smallholder livestock farmers. This study was done to examine linkages between women’s empowerment and access and control over livestock products and vaccines. The Women Empowerment in Livestock Index (WELI) tool, which was customized to include questions on livestock vaccine access, was used to capture baseline data on empowerment scores for women in Machakos county, Kenya, prior to implementation of animal health and vaccine test models. In total, 400 participants were surveyed in two wards of Machakos County, Kola and Kalama, which were purposively selected. Women’s empowerment was mapped to three domains (3DE): intrinsic agency (power within), instrumental agency (power to), and collective agency (power with) measured against adequacy in 13 indicators. Our results indicate that the household structure (female headed or dual headed household), age of respondents and number of members in a household influence the adequacy score. Work balance was the most significant negative contributor to women’s disempowerment. Women contributed the most to livestock productive activities and attained adequacy in this area compared to men, directly impacting the WELI score. Women smallholder livestock farmers report low CCPP and ND vaccination rates, minimal knowledge on livestock diseases, a lack of access to cold chain storage and rarely visited veterinarians. The WELI score was 0.81 indicating a high level of empowerment for women in this community compared to men leading us to conclude that the overall WELI score was not an accurate indicator of women‘s empowerment in Machakos County. However, the decomposability of the index allows us to disaggregate the drivers of change and to examine how individual indicators contribute to disempowerment.