The last decade has seen rapid evolution in guidance from the WHO concerning the provision of HIV services along the diagnosis-to-treatment continuum, but the extent to which these recommendations are adopted as national policies in Kenya, and subsequently implemented in health facilities, is not well understood. Identifying gaps in policy coverage and implementation is important for highlighting areas for improving service delivery, leading to better health outcomes. We compared WHO guidance with national policies for HIV testing and counselling, prevention of mother-to-child transmission, HIV treatment and retention in care. We then investigated implementation of these national policies in health facilities in one rural (Kisumu) and one urban (Nairobi) sites in Kenya. Implementation was documented using structured questionnaires that were administered to in-charge staff at 10 health facilities in Nairobi and 34 in Kisumu. Policies were defined as widely implemented if they were reported to occur in > 70% facilities, partially implemented if reported to occur in 30–70% facilities, and having limited implementation if reported to occur in < 30% facilities. Overall, Kenyan national HIV care and treatment policies were well aligned with WHO guidance. Policies promoting access to treatment and retention in care were widely implemented, but there was partial or limited implementation of several policies promoting access to HIV testing, and the more recent policy of Option B+ for HIV-positive pregnant women. Efforts are needed to improve implementation of policies designed to increase rates of diagnosis, thus facilitating entry into HIV care, if morbidity and mortality burdens are to be further reduced in Kenya, and as the country moves towards universal access to antiretroviral therapy.