To effectively address high malnutrition burden in Zambia, health systems must be strengthened to deliver an effective continuum of care. This paper examines health system services in relation to nutritional support for children under-five years, in order to identify gaps and propose interventions. We utilized data from a study on factors associated with severe acute malnutrition in under-five children to assess health facility nutrition services offered at select level-one hospitals in five provinces in Zambia. Stata was used for analysis. We conducted univariate analysis to assess nutrition services offered, functionality of equipment and tools, availability of human resource and human resource development, and availability of drugs used for assessment and management of nutrition-related health outcomes. We found large variations in the level of nutrition services offered across districts. Of all hospitals sampled, 88% provided group nutrition counseling and 92% offered individual nutrition counseling to their clients. Overall, the existence of referral and counter-referral systems between the community based volunteers and hospitals were the lowest among all services assessed at 48% and 58% respectively. We also found inadequate numbers of human resource across all cadres with an exception of nutritionists. This study has revealed a number of gaps in the health system and health service delivery to be addressed; most notably, lack of tools, policies and guidelines, drugs and health specialists to help care for malnourished infants and children. Achieving universal coverage for nutrition services in Zambia will require more attention to the health systems issues found in this study.