This study examines the relationship between malaria incidence and infant mortality in Uganda using quarterly data from 2000–2024 obtained from the World Bank. The variables were transformed into natural logarithms to reduce extreme variations and improve data stability. A cointegration approach was employed, with infant mortality rate (per 1,000 live births) specified as the dependent variable and malaria incidence (per 1,000 population at risk) as the independent variable. The normalized cointegrating vector revealed a negative long-run relationship between malaria incidence and infant mortality, implying results that contradict theoretical expectations. This suggests that other structural factors, including weak health infrastructure, malnutrition, and other childhood or prenatal infections, may play a more significant role in explaining infant mortality in Uganda. The error correction coefficients were negative and statistically significant, confirming long-run equilibrium adjustment and the existence of cointegration between the variables. Furthermore, Granger causality results indicated no significant predictive relationship from malaria incidence to infant mortality. The study recommends strengthening broader maternal and child healthcare interventions alongside malaria control programs.