Interrupting vertical transmission of HIV from mothers to infants provides opportunity to transform the HIV/AIDS epidemic by eliminating new infections among children. We estimate mother-to-child transmission rates of infants born to known HIV-positive mothers offered prevention of mother-to-child transmission interventions and provide an indication of Kenya’s progress toward elimination of perinatal transmission. We obtained from the Kenya National Early Infant Diagnosis (EID) database, all 131,451 DNA polymerase chain reaction test results of HIV-exposed infants aged 0–18 months who had dried blood spot samples taken between January 2008 and October 2013. The majority of samples were from infants aged 0–6 months (81.0%). Infants aged 6–12 months comprised 15.5%, while those aged 12–18 months were 3.5%. Overall, 11,439 (8.7%) were HIV-positive. Positivity rates were higher among older age groups: 6.8, 14.6, and 27.5% in age groups 0–6 months, 6–12 months, and 12–18 months old, respectively. In Kenya, scale-up and decentralization to primary health centers of EID services has been remarkable. Both increasing HIV-positivity trends in age groups 12–18 months and differences between provinces require further interrogation. Although significant, declining HIV-positivity trends in age groups 0–6 months and 6–12 months old observed between 2008 and 2013 is insufficient to achieve the elimination agenda.