Milk production by smallholders in Africa has a high carbon footprint (CF) and is predicted to increase significantly in the coming decades. This study, based on data from a sample of 382 farms in central Kenya, is the first assessment of the CF of milk production in Sub-Saharan Africa based on a large dataset of actual farm management practices. The aims of the study were (1) to determine whether there are significant differences in the CF of farms with different feeding systems (i.e., zero-grazing, grazing and mixed systems), and (2) to identify factors associated with variability in CF between farms. This analysis is used to identify options for mitigating GHG emissions from Kenya’s growing dairy production. Average CF ranged between 2.19 and 3.13 kg CO2e/kg fat and protein corrected milk (FPCM), depending on the GWPs and allocation method used. Analysis based on variability in farm management showed that CF was similar between farms with zero-grazing and mixed feeding systems, and significantly higher on farms with grazing only feeding systems, but no difference was detected when input parameter uncertainty was considered. At individual cow level, variation in milk yields explained more than 70% of the variation in GHG intensity. At farm level, milk yield explained less than half of variation in CF. CF was correlated with feed characteristics, manure management practices and herd size and composition. In particular, the level of concentrate use was positively correlated with CF, and was the most important factor explaining variation in CF not attributable to variation in milk yield. Our findings suggest that promoting balanced feed rations and feeding concentrate according to cows’ needs across the lactation cycle could provide opportunities to both increase milk production and reduce the CF of milk production on smallholder farms in central Kenya. Supporting smallholder farmers to implement these mitigation options will require interventions at several levels in feed supply chains in the dairy sector.