The optimum production in dairy cows aims at getting a calf per cow per year. This, however, is limited by repeat breeding syndrome (RBS), which has multiple etiologies that cause either fertilization failure or early embryonic death. This study objective was to determine the prevalence of repeat breeding syndrome in dairy cattle within the selected regions of Kenya. A cross-sectional study design was carried out in 205 smallholder dairy farms in Makueni, Kakamega and Nandi counties. A total of 553 cows/heifers were recruited and examined per rectal to determine their reproductive status. Information on the breeding history of the cow and heifer was acquired at the farm. The results revealed that cross bred cattle were most affected by RBS at 38.9% followed by Jersey, Guernsey Ayrshire and least in Frisians at 21.1, 16.7, 25 and 14%, respectively. The overall animal level prevalence of RBS in cattle in the three counties was at 18.4%, while the overall farm-level prevalence was 58.3%. However, per county prevalence’s were different with animal level prevalence at 31.9, 20.9 and 12.5% in Makueni, Kakamega and Nandi, respectively. The farm-level prevalence’s at the counties were 75.4, 58.3 and 48.4% in Makueni, Kakamega and Nandi counties, respectively. Cattle kept in the zero-grazing/intensive system had the highest level of RBS at 30.1% compared to semi-intensive and extensive farming systems. The prevalence of RBS was also higher in multipara at 76% in comparison to primipara cows. Finally cows over four years which were in third or more parities had the highest prevalence of RBS, accounting for 65%) of the cases. In conclusion, the prevalence of RBS is significantly high in the Kenyan smallholder dairy farms. Further research should be undertaken to identify risk factors and appropriate intervention approaches for RBS to enhance its management.