A key bench mark of successful therapeutic policy implementation, and thus effectiveness, is that the recommended drugs are available at the point of care. Two years after artemether-lumefathrine (AL) was introduced for the management of uncomplicated malaria in Kenya, we carried out a cross-sectional survey to investigate AL availability in government facilities in seven malaria-endemic districts. One of four of the surveyed facilities had none of the four AL weight-specific treatment packs in stock; three of four facilities were out of stock of at least one weight-specific AL pack, leading health workers to prescribe a range of inappropriate alternatives. The shortage was in large part caused by a delayed procurement process. National ministries of health and the international community must address the current shortcomings facing antimalarial drug supply to the public sector.