Zanjani is known for being the first and only cleric president of University of Tehran. Zanjani hold no secular academic degree and was appointed by Mohammad Mehdi Zahedi, the minister of Science, Research, and Technology in Mahmoud Ahmadinejad's cabinet in 27 December 2005. Before his selection, the president of the University of Tehran was elected by the faculty members. After his establishment as the president of University of Tehran, many students protested in front of the Central Library, where the establishment ceremony was holding.
At the time of his appointment as the chancellor of Tehran University, Zanjani was a lecturer with a ranking equivalent to "associate professor". However after his appointment, He and his allies tried to make a fake academic degree and university ranking for him. As an example Tehran University launched a webpage about his background education, claiming that "he holds a PhD degree from University Elites, Iran".
Zanjani is a member of the Board of Directors of Imam Khomeini International University. He has published more than 40 books and 70 articles in local newspapers and journals. He is also the founder of the Research Center for Studies and Researches on Islamic Sciences.
During his post as the president of the university, Zanjani was repeatedly criticized for his mismanagements by students and academics. On 5 February 2008, Zanjani was replaced by economist academic Farhad Rahbar after three-days demonstration organized by Tehran University students.
Zanjani has strong political ties with Iranian conservatives and a member of Combatant Clergy Association. Amid Zanjani has had an active presence in reconsideration of the Constitution in 1989 as the delegate of the Parliament in the Revising Council. He has served as a member of Islamic Parliament from Tehran for two terms.
In 2006, the Ahmadinejad government systematicly forced numerous Iranian scientists and University professors to resign or to retire. It has been referred to as "second cultural revolution". The policy has been said to replace current professors with younger ones. Many University professors received letters indicating their early retirement unexpectedly.