In Uganda's government departments, anti-corruption policies have been implemented to curb corruption but their effectiveness remains questionable. The research employs comparative analysis with specific focus on qualitative feedback data collected from government departments in both countries. A notable theme identified was the significant improvement in transparency protocols and whistleblower protection mechanisms observed in Rwanda compared to Uganda, indicating a need for further reinforcement in Uganda’s implementation strategies. The findings suggest that while Rwanda has made strides in implementing anti-corruption policies, there is room for improvement in Uganda's efforts. The study recommends strengthening enforcement mechanisms and enhancing public awareness campaigns. Recommendations include the development of robust whistleblower protection laws, increased transparency in government processes, and enhanced training programmes for public servants to foster a culture of integrity.