Enterprise Resource Planning (ERP) systems implementation is increasing rapidly in the higher education institutions, because of the call by various governments on them to streamline processes and functions. However, not all ERP implementations have been successful. There are still challenges in the implementations of ERP especially in the higher education sector. Since ERP implementation comes with high cost and also affects every aspects of the institution, there is therefore the need of investigating the challenges of ERP implementation in HEIs. The study focuses on ERP implementation challenges in the Ghanaian higher education. Using a case study research, data for analysis were collected from some public universities in Ghana and were analyzed using inductive thematic analysis. The findings of the study revealed three categories of challenges: institutional related challenges, financial related challenges and human related challenges. It is expected that the findings of this study would provide valuable information not only to practitioners but also to academics. The findings will serve as source of general guidance in stimulating future research in this area. Understanding these challenges will assist HEIs to eliminate or mitigate ERP implementation failures.