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Universities play a crucial role in the development of any nation. The success of Higher Education Institutions (HEIs) is the bedrock of the growth in human capacity required to support the growth of an economy. However, HEIs have been criticized for not playing their rightful role in national development. This has been partly attributed to not being able to manage their performance in view of the dynamic and turbulent environment they are operating in. Most HEIs have been caught up in the “business as usual” situation preferring doing things in the traditional ways as opposed to changing with the times. As a result their survival has been at risk especially from those HEIs who have adopted the “business un-usual” mentality. It is as a result of the challenges facing Kenyan HEIs that this paper proposes an adoption of the Balanced Scorecard as a management tool in HEIs. This paper provides a review of literature on the HEI environment globally and in Kenya, highlighting the challenges faced by Kenyan HEIs and proposes the use of the BSC to address the same. The BSC is a tool that helps mainstream the vision and mission of HEIs in their activities thus making the HEIs become strategy focused organizations. The BSC is a strategic planning and management system used to align business activities to the vision and strategy of the organization and to monitor organization performance against strategic goals. Finally, a sample BSC for HEIs in Kenya is proposed. It is felt that if HEIs focused on the issues proposed and measured their performance on the issues identified, their performance will be improved tremendously.