This project looks at the Application of separation of powers in a presidential system of government. Separation of power in the presidential system of government is a system of government where the executive branch of government exist alongside with the legislature and the judiciary serves as watchdogs. The objective of this study is to find out whether the separation of powers in Nigeria presidential system of government from 1999- 2014 has helped to improve the civil liberty and freedom of citizens in Nigeria but it was discovered that the separation of powers preached in Nigeria does not guarantee civil liberty and freedom of citizens since 1999-2014. From the study, the following findings are drawn from this research work. 1) That the Nigerian presidential system of government does not encourage tyranny and abuse of power due to the fact that there is a separation of powers. 2) That the separation of power is partly due to the fact that Nigerian is a developing nation which is characterized by high level of corruption.