Malaria is a serious public health problem in over 90 countries worldwide. In Brazil the disease is prevalent in the Amazon and the control rationale is based on early diagnosis and treatment. Quality pharmaceutical services are considered a key element for control. A proposal for evaluating pharmaceutical services for malaria is presented here. A theoretical outline composed of a logical model and an indicator framework is discussed and strives to establish a basis for assessment and judgment of the way in which these services are actually delivered. The aim is to contribute to the understanding of pharmaceutical services for malaria and other endemic diseases, complying with the directives of the Brazilian National Medicines Policy.