As far as could be established, no empirical study had been conducted with the aim of designing a performance management model for systematically managing institutional performance at public universities in Uganda. The purpose of this study therefore, was to develop an institutional performance management model for universities in Uganda. This was achieved by establishing: the extent to which public universities in Uganda implemented institutional performance management, the challenges impacting institutional performance management implementation in universities in Uganda, how public universities could ensure effective institutional performance management implementation, the various measures of institutional performance that are applicable to universities in Uganda and the key components of the institutional performance management model that could be adopted by universities in Uganda in managing institutional performance. A mixed methods approach was adopted, applying both the qualitative and quantitative methodologies. Phenomenology and cross sectional survey strategies were adopted. Interviews were conducted with purposively selected top administrators of a selected public university and the results informed the survey questionnaire. This instrument was later administered to academic staff in four public universities using a disproportionate stratified random sampling technique. The findings revealed that strategic planning in public universities in Uganda does exist and it is aimed at achieving quality. Despite the existence of strategic planning, academic staff are uncertain about a number of issues related to strategic planning. Respondents generally disagreed that: performance management training is continuously provided to managers and staff, they have an effective performance management system and a formal process exists for units to provide feedback on the attainment of goals. Among the challenges impacting performance management implementation in universities in Uganda was: (i) Lack of a formal performance management environment; (ii) Limited employee engagement/communication problems; (iii) Institutional systems and structural challenges; (iv) Institutional governance challenges. The identified factors for the successful implementation of institutional performance management were categorised into four groups namely: (i) A performance framework, performance culture and employee support; (ii) An individual performance management system; (iii) Alignment; (iv) SMART goal setting. The study established that performance measures for public universities in Uganda could be categorised into five categories namely: (i) Leadership practices, infrastructure and academic profile; (ii) Accountability; (iii) Involvement with external stakeholders; (iv) Information and knowledge transfer; (v) Strategic implementation. Finally, the proposed performance management model consisted of three phases namely: (i) Designing the strategy; (ii) Implementation of the strategy; (iii) Evaluating rewarding and improving performance. University managers should pay close attention to the identified challenges while ensuring that the factors that facilitate successful performance management implementation are in place. The measures identified by this study could be used by policy makers and universities to determine the extent of performance of the various universities, not only in Uganda but also in sub-Saharan Africa and the proposed model could be adopted by universities in Uganda as well as by all institutions of higher learning during institutional performance management implementation. Ultimately, the success of the implementation process is vested fully in the commitment and willingness of management and the employees to participate in the entire process right from the design stage to the evaluation stage.