Leadership is a field of study that has been studied in management and organizational development for a number of years. It is becoming increasingly important to study leadership in the context of higher education institutions, especially in the African context. Kenya is currently experiencing a crisis in higher education with lecturer’s strikes in public universities and students strikes in some private universities that have consequently led to university closures. The role that leadership plays in this is hard to ignore. That is why this study sought to investigate the link between leadership and performance and the differences between male and female leaders in higher education institutions in Kenya. The study employed descriptive research design targeting 74 accredited universities in Kenya. The population was distributed into 5 distinct groups from which a sample of 43 universities were selected to be studied. Stratified sampling technique was used to attain the required sample size. This study adopted a quantitative approach to assess leadership style of top management and performance of universities in Kenya. Both students and staff were subjected to the study in order to provide data on the link between leadership and performance in their respective institutions. In addition, there is not a large amount of literature on the link between leadership and performance in universities, in the African context. The study concluded that leadership styles affect the performance of universities in Kenya. Transformational and transactional leadership were found to have a significant association with performance of universities in Kenya. The study recommended emphasis on transformational leadership and transactional leadership in universities to boost performance of studied institutions.