A comprehensive and integrated assessment of health-system functioning requires measurement of universal health coverage (UHC) for disease-specific interventions. This paper aims to contribute to measurement of UHC by utilizing locally available data related to malaria in Nepal. This paper utilizes the elements of UHC as outlined by the World Health Organization (WHO). The concept of UHC represents both improvements in health outcomes and protection of people from poverty induced by health-care costs. Measuring UHC focusing on a tropical disease highlights the progress made towards elimination of the disease and exhibits health-system bottlenecks in achieving elimination of the disease. Several bottlenecks are found in the Nepalese health system that strongly suggest the need to focus on health-system strengthening to shift the health production function of malaria intervention. The disaggregated data clearly show the inequality of service coverage among subgroups of the population. Analysis of effective coverage of malaria interventions indicates the insufficient quality of current interventions. None of households faced catastrophic impact due to payment for malaria care in Nepal. However, the costs of hospital-based care of malaria were not captured in this analysis. The paper provides the current status of UHC for malaria interventions and reveals system bottlenecks on which policy-makers and stakeholders should focus to improve Nepal’s malaria control strategy. It concludes that financial coverage of the malaria intervention is at an acceptable level; however, service coverage needs to be improved.