Separation of powers is one of the fundamental principles of governance in modern legal systems, which aims to prevent the concentration of power and guarantee public freedoms. This principle has different manifestations in the thought of Jean-Jacques Rousseau and the legal system of the Islamic Republic of Iran. By emphasizing the public will, Rousseau introduces the separation of powers as a means to realize the sovereignty of the people. He believed that the legislative branch, which is the manifestation of the public will, has a superior position and the executive branch is the only agent for implementing laws. In contrast, in the legal system of the Islamic Republic of Iran, the separation of powers is accepted with a relative approach. According to Article 57 of the Constitution, the legislative, executive, and judicial branches are independent of each other, but are under the supervision of the Supreme Leader. This supervision, through the position of Velayat-e-Faqih, creates a kind of coordination between the powers, which is different from the concept of absolute separation of powers in Rousseau's thought. A comparative study of these two approaches shows that in Rousseau's thought, direct democracy and the general will are the main axis of governance, while in the Islamic Republic of Iran, a combination of democracy and jurisprudential principles is presented in the form of Velayat-e-Faqih. The results of this study indicate that although both systems seek to prevent the concentration of power, the difference in philosophical and legal foundations has led to differences in the way in which the separation of powers is realized.