The main purpose of this paper is to identify and analyze State-building and Institutionalization in the political thought and practical conduct of Ayatollah Khamenei (the Islamic Republic of Iran). In order to answer this paper's questions, we have used document analysis method, which is one of qualitative methods, to review available documents including books, articles, theses, etc. By examining the political thought of Ayatollah Khamenei, such parameters as paying attention to the society's values, political crises, and special circumstances of the time, which have been influential in his Institutionalization, are considered. It can be said that Institutionalization has a special situation in the political thought and practical conduct of Ayatollah Khamenei. So, after examining his political thought, we will try to present some evidence of Ayatollah Khamenei's Institutionalization based on various functions and with regard to the parameters mentioned above separately. Introduction and establishment of political, legislative, judicial, scientific-cultural, military, and service institutions on a temporary or permanent basis are among the evidence of Institutionalization under the leadership of Ayatollah Khamenei.