Participatory monitoring and evaluation (PME) is an approach that higher education institutions should use to ensure achievement of objectives especially quality academic programs, research, consultancies, outreach services and administrative functions. Indeed, over the past 10 years PME has gained increased prominence over more conventional approaches to monitoring and evaluation in public management, corporate management, business management and project management. PME process can enhance participation, empowerment and governance, thus enhancing the performance, efficiency and sustainability of interventions. Uganda developed a National Monitoring and Evaluation Policy for the Public sector, which provides a framework for all public sector entities to follow up their performance. However, the policy is not well disseminated and public sector entities are not sufficiently compelled to undertake participatory monitoring and evaluation as an approach. This paper analyzes the role played by PME to ensure quality programs in higher education institutes in Uganda. It draws conclusions and proposes remedy on what is still hampering effective participatory monitoring and evaluation practices in Uganda's higher education institutes.