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This study aims to explore incubatees’ perceptions of the challenges facing start-ups and entrepreneurs at the National University of Lesotho Innovation Hub. An interpretive, qualitative approach was adopted. Six purposively selected incubatees partook in semi-structured interviews and the data were analysed through content thematic analysis. Delay in disbursement of incubation funds, infrastructure deficits and deficiency of entrepreneurial knowledge were identified as the major constraints as perceived by incubatees. University hubs should ensure that capitation grants are disbursed to the start-ups on time to provide incubateess’ timely preparation of the budgets and purchase of all the required products and hence timely commencement of the incubation process. Lack of essential facilities in the university hub and deficiency of entrepreneurial knowledge may hinder the ability of start-ups to successfully develop. The study results suggest the development of strategies and initiatives to effectively support start-ups in university hubs. Benchmarking from successful experience of regional and international universities innovation hubs on how to effectively manage incubator sponsorship. Implementation of training and development programs to assist start-ups to acquire new skills and stay updated with the latest industry trends and technologies. Lastly, investment in contemporary facilities, such as labs, offices and provision of state-of-art resources for incubatees is commended.