The paper focuses on assessing and identifying the factors that affect the morale of employees in the institution of higher learning in South Africa. Employee morale is a drive to keep the organisation growing and achieve its objectives. In the worldwide ranking there are two institutions of higher learning that are featured in the top 250 of the universities which could be the result that employees are engaged in their institutions. However, it is imperative to maintain or improve more by understanding and dealing with the factors that may contribute negatively in the institutions of higher learning in SA. A quantitative approach was utilised for the paper and a questionnaire was constructed to collect data from 108 academics and support staff. A stratified approach method wad used and divide participant into groups academics and support employees. All data collected was analysed using SPSS version 22 and the findings of the paper reveals that the level of employee morale was very low and further reveals that management support and feedback, conditions of work, remuneration packages, benefits, promotion processes and recognition, communication and understanding of policies as well as treatment and workload were the crucial factors affect the morale of employees. The paper recommends that all institutions of higher learning to review their own policies and ensure that all stakeholders of their institutions understand them effectively. Similar research should be conducted in other institutions of higher learning as well in order to generalise or enrich the findings of the present paper which serve as a wake-up call.