African universities have to play a central role in Africa’s development through the provision of quality training, knowledge and innovations. This is particularly crucial in ensuring a food secure Africa through a knowledge-based transformation of agriculture and related activities. Information on the state and challenges of higher agricultural education can inform actions aimed at positioning institutions to play the roles expected of them. The overall objective of this study was to assess the current status of the higher education sector in Ghana to identify current challenges and gaps and develop specific recommendations towards enhancing its performance and contribution to science, technology and innovation. Focusing on the five main public universities in Ghana, the study comprised a desk research and interviews with key officials of selected institutions. The findings suggest low quality of service to students due to large gaps in funding, teaching staff, and academic facilities.The demand for higher education in general far exceeds the supply. The total number of applicants to agricultural programmes increased sluggishly between 2004 and 2014, with female applicants hovering around 20%. Funding gaps, low technical or infrastructural capacity and declining number of applicants to science, technology, engineering and mathematics programmes are key issues that require urgent attention.