The Mongol invasion caused great devastation and significant social change in the eastern parts of the Islamic world, where scientific organizations did consequently suffer irreparable damage. Using ahistorical-comparative method, the present paper purported to study the model of reconstruction of scientific organizations in post-Mongol invasion era in Iran with emphasis on Rabe Rashidi University of Tabriz. Given that the institution of ‘science’ for flourishing and sustaining the continuum of progress requires the constant presence of a conducive social and political context as well as economic foundations and institutionalized knowledge-oriented values in society, after the Mongol invasion and positioning of Tabriz as a political center and capital city, Rashid al-Din Fazlullah Hamadani in the capacity of Ilkhanid chancellor expended a great deal of effort to contribute to the development and management of each of the afore-mentioned elements. He aptly combined and augmented the efficacy of the then available ‘raw materials’ via molding them into an educational organization and reframed the dispersed and informal endowments into a formal academic organization to be utilized by the educational departments and all those involved in Rabe Rashidi. Preparing a conducive educational environment, delineating organizational goals, organizing the space and time of the training groups, developing educational curricula, planning for the methods and quality of teaching, managing classes, and assigning students into cohorts according to their talents and interests were some of the management skills of Rashid al-Din, just to name some. The accomplishments of Rabe Rashidi University in acquiring Chinese and Mongolian sciences and integrating them into the legacy of Islamic sciences besides its special relationship with Byzantium had made Rabe Rashidi one of the channels for the transfer of Islamic knowledge to Europe.