The study examined the effect of malaria incidence and malaria control on health outcome and human capital development in Nigeria for the period of 1991 to 2017. The Vector Error Correction Model (VECM) was employed for analyzing the objectives of the study which include to examine the effect of malaria incidence on adult mortality rate, under-five mortality rate, and human per capita income in Nigeria, and to examine the effect of malaria control on malaria incidence in Nigeria. The findings of the study revealed thatNigeria among other African nations is yet to fully achieve the objective of reducing the burden of malaria and effectively controlling the prevalence of malaria, thereby improving on positive health outcomes and sustainable national development, as the VECM analysis of empirical results showed that malaria incidence had a positive but minimal effect on adult mortality rate by 0.5%, under-five mortality rate by 0.8%, and human per capita income by 40%. It also showed that malaria control which consists of children receiving anti-malarial drugs, government health expenditure, and insecticide-treated bed nets (ITNs) had a positive but poor effect on reducing the prevalence of malaria in Nigeria. As a result, the study recommends that the current National Malaria Control Programme (NMCP) should be strengthened and given more impetus in order to effectively control and combat malaria, the federal government of Nigeria should give major priority to the health sector in terms of spending as this will increase the provision of health facilities, storage facilities, and provision of appropriate anti-malarial medicines that will aid in controlling and reducing malaria incidence in Nigeria, among others were proffered.