The study investigated the university staff's perception on deregulation of higher education in Nigeria. Descriptive research of the survey type was used for the study. The population comprised all the university staff of universities in Ekiti and Ondo states, Nigeria. Simple random sampling technique was used to select 700 academic and non-academic staff from the Federal and State universities in Ekiti and Ondo states. Research instrument designated University Staff Perception of Deregulation on Higher Education (USPDHE) was used in collecting data. The questionnaire was subjected to face and content validity. The reliability co-efficient of the instrument was 0.75. The results showed that deregulation improved academic standard of the universities except in the areas of curriculum innovation and collaborative research and does not guarantee job security nor improve staff development and equity in salary structure but it contributed to managerial effectiveness, efficiency and accountability, It also showed that students were affected in the area of access to higher education, class structure, admission choice and exploitation by the institutions. It equally showed that deregulation is not improving the funding of higher institutions in Nigeria instead it throws the institution into dilemma of sourcing for fund. Some of the recommendations are: using management strategies at the institutional level, autonomy should use management strategies that emphasize improved standards in terms of improved curricula, and academic excellence by all and sundry within the system. Also, to have the full gains of deregulation, climate of academic integrity should be enshrined in the operation of the university system.