Public health surveillance systems are critical for monitoring disease prevalence and guiding intervention strategies in Uganda. A systematic literature review was conducted to assess the methodology used in studies evaluating public health surveillance systems for clinical outcome measurement. The analysis identified a mixed pattern of methodological rigor across studies, with some demonstrating robust use of statistical models and confidence intervals (e.g., $SE = 0.5$). While the majority of studies used quasi-experimental designs for measuring clinical outcomes in Uganda's public health surveillance systems, there is room for improvement in methodological consistency. Enhanced training programmes and standardised methodologies should be implemented to improve the reliability and validity of data collected by these surveillance systems.