Nowadays, universities and higher education institutions have a critical role in developing countries and it is essential that their performance is evaluated with appropriate methods and criteria. Among the various functions of universities, research and scientific production is the most important one. The evaluation of scientific outputs is an attempt to assess the performance of universities. The use of scientometric indicators is a way to assess the scientific outputs of universities. In this context, a number of indicators have been defined to assess the quantity and quality of scientific outputs of researchers that can be extended to assess the institutions. Through a descriptive survey, in this paper, 285,526 scientific outputs of 76 universities affiliated to Ministry of Science, Research and Technology were selected and evaluated. The data of each university were analyzed individually using the indicators such as the number of scientific outputs, number of citations, h-index, m-parameter and g-index and the institutions were ranked. The results show that Tehran University in number of scientific outputs and number of citations, Sharif University of Technology in h-index and g-index, and Babol Noshirvani University of Technology in m-parameter are as the top Iranian Universities in the surveyed universities. The overall ranking shows that Tarbiat Modares University and Sharif University of Technology are top. Finally, we compare and discuss our ranking results with ISC and URAP ranking systems. The results show that the ranking of universities in this research in terms of the number of scientific outputs, the number of citations, h-index and g-index has a high correlation with that of ISC and URAP systems.