Public health surveillance systems in Uganda are crucial for monitoring infectious diseases to prevent outbreaks and improve public health outcomes. A multilevel regression model was employed to assess system performance at both national and regional levels, accounting for variability in surveillance data. The model revealed that increasing funding by 10% at the district level significantly improved disease detection rates (OR = 1.23; CI: 1.05-1.47). This study provides a robust framework for optimising public health surveillance systems in Uganda, with specific recommendations for resource allocation. Public health authorities should prioritise additional funding to high-risk districts identified by the model.