We assessed programmatic gaps that prevent the optimal treatment of pediatric HIV infection despite free antiretroviral care in Kenya. Of 626 HIV-infected Kenyan children, the median age was five years, 54% were male and the mortality rate was 3.2 per 100 person-years. A total of 380 (61%) children initiated antiretroviral therapy (ART) during the study period. Among the 246 children who never started ART, 129 (52%) met the criteria for ART initiation. Immunologic failure occurred in 20% of children who received ART for >24 weeks. In multivariate analysis, immunological failure was associated with having nonimmediate relative or unrelated caregivers accompanying the child to clinic (AOR = 69.16, p = 0.008). Having ≥ 3 types of accompanying caregivers was also associated with virologic failure in multivariate analysis (AOR = 3.84, p = 0.03). The lost to follow-up rate was 8.7/100 persons-years for the entire cohort, and significantly higher (17.7/100 persons-years) among children not on ART (p < 0.001). Among children who do initiate ART, those with the best treatment outcomes were those who had a limited number of close relatives as caregivers and good adherence to ART. Focus on early ART initiation and education of the right caregiver will likely improve retention and quality of pediatric HIV care in Kenya.