Hajjarian was born in Javadiyeh neighborhood of Tehran, Iran in 1954 to parents from Kashan. He studied mechanical engineering at Tehran University. In 1977 Hajjarian was enrolled for military service in Gendarmerie. A young Iranian revolutionary during the 1979 Iranian Revolution, he entered the Islamic Revolution Committees before becoming an Intelligence officer in Navy. Hajjarian contneud his education and obtained a Ph.D. in political science from Tehran University. His thesis advisor was Hossein Bashiriyeh. He was one of the students who took over the US embassy in Tehran in 1979.
After the revolution, Hajjarian was involved in the formation of the intelligence apparatus of the newly founded Islamic Republic. Through the 1980s, he worked in the ministry of intelligence, where his positions included vice minister for political affairs. In the late 1980s, he left the ministry, and established Center for Strategic Research under the presidency. That was where he played an important role in creating a new discourse based on democracy and rule of law for his generation of revolutionaries.
When Mohammad Khatami was elected President in 1997, he appointed Hajjarian his political advisor. In 1999, he was elected to the city council of Tehran in the first city elections after the 1979 revolution. Hajjarian was also the editor of Sobh-e Emrooz newspaper, which was a strong advocate of Khatami's reforms. He was believed to be the source of information for many articles written by the investigative journalists, Akbar Ganji and Emadeddin Baghi. These included stories about the "Chain murders" of dissident intellectuals by members of Iran's intelligence ministry.
Hajjarian was one of the personal key factors of president Khatami. He was a member of the reformist elite and has leadership support role in reform movement. He joined the ministry of intelligence and national security (MINS) in 1984 and he leaves it in 1989. He worked also in the center of strategic studies. Working in such a place, he was able to invite some of the officials of MINS to join the reform movement. All of them try to develop the reform movement. Peoples like kbar ganji, Mohsen Armin, Abbas abdi, Hamid Reza Jalaeipour, Muhammad Mousavi Khouiniha, Ebrahim Asghar zadeh and Mohsen Sazgaran are among those personals.
In March, 2000 he was shot in the face by a gunman on the doorstep of Tehran's city council. The would-be assassin fled on a motorcycle with an accomplice. The bullet entered through his left cheek and lodged in his neck, and put Hajjarian into a coma. During this time, groups of young Iranians kept vigil outside Sina hospital, where he was being treated. Hajjarian was badly paralyzed for life.
His assailant, Saeed Asgar, a young man who was reported to be a member of the Basij militia, was later arrested and sentenced to spend 15 years in jail. But he was released after spending only a short term in prison. Asgar was accompanied by Mohsen Morteza Majidi on a motorbike. Others, who were involved, include Mohammad Ali Moghaddami, Mehdi Rowghani, Mousa Jan Nesari, Ali Pourchaluei (possibly the one who shot Hajjarian), Saeed Golounani and Safar Maghsoudi.
His attempted assassination is thought to be associated with the exposure of the "Chain murders" in his Sobh Emrouz daily newspaper, and the "key role" he is believed to have played "in bringing about ... damaging disclosures," both as the editor of the exposing newspaper and one of the few reformists likely to be a source of information about activity in the intelligence ministry. Consequently, "some believe that remnants" of the chain murder "intelligence killer group may have been" behind his attempted assassination.
Hajjarian slowly recovered somewhat from the shooting. By 2005, Hajjarian was still unable to speak with a clear voice and still using the wheelchair, although could walk with help. As of 2009 he still spoke with difficulty and was "dependent on the constant care of doctors and family."
Hajjarian has used the term “dual sovereignty” as an analytic tool to describe the balance of power in the Islamic Republic's government system, in which there is a supposed split between the Supreme Leader and popularly elected officials, e.g. the President. The idea has been publicly denounced by Ali Khamenei in 2004, being called "damaging and a deadly poison" repeated by "irrational people".
He believes that a frontal assault on the fortresses of power is impractical. Hajjarian argued that domination of politics by clerics was wrong, but could be gradually eroded by "mobilizing the masses and using them as bargaining chips with Iran's rulers." His strategy for the reform movement was described as extending the reformists "reach by triangulating between the mass movement they represented and the autocratic state with which they shared power. He coined the phrase that would define the reformists’ strategy: “Pressure from below, negotiation at the top.” The strategy remarks that by developing civil society and winning the battle of public opinion, the reform movement can gain enough strength to not only resist the hardliners, but also push for deep changes within the system via bargains with top officials unwilling to reform.
Hajjarian formulated the proposed gradual move to a favorable democratic system as “fortress to fortress triumph”, meaning that reformers should concentrate on weakening and capturing key institutions, i.e. fortresses of power, one by one.
Hajjarian argued that there is a way of combating the predominance of Valiyat al-faqih (rule of the Islamic jurist) by underlining the de facto secularization of religion by the supreme leader of the Islamic Republic, Khomeini. He allegedly showed the supremacy of politics as such over any religious norm when he said that the interests of the Islamic Republic are paramount in Islam and that zakat, salat, hajj, and everything else in Islam, are subordinant. This kind of decision, he states, means that politics are more important than religion and that this acknowledges the secularization of religion. In this context, he argues, it is possible to reassess velayat faqih and to reject its supremacy within the political field in Iran.
After reformists lost their "fortresses", Hajjarian said in 2004 that the reforms program have been failed and now there are multiple choices for the Iranian people. One option is giving up and accepting the current situation. Another choice is apathy, followed by adopting defeatism—waiting for a possible foreign military action against Iran and regime change— or to let the developing lumpenproletariat in the society grow until they ignite a revolution in Iran. Hajjarian prefers what he calls the best alternative, which is to assume “reforms is dead, long live the reforms” and continue the reforms path patiently.
On 16 June 2009, four days after the disputed presidential election, it was reported that Hajjarian had been arrested. It was reported that he died in Evin prison under torture on 7 July. However, it was later added that he was still alive but had suffered a nervous breakdown on 8 July and was in critical condition in a military hospital in Tehran. Later, there were reports that he was still in Evin Prison, possibly in a clinic there, and that according to his wife, physician Vajiheh Marsoussi, his medical condition was "deteriorating severely" while in prison. Hajjarian was accused of having links with the British intelligence service on 25 August 2009.
In May 2015, Hajjarian was allowed to give a short speech at University of Tehran. According to the reformist Shargh Daily, enthusiasm for the speech was so great that seats were filled up hours before the event. In a note he gave to a student to read, Hajjarian stated that the 1997 presidential election were the reformists prevailed were the first since the 1979 Iranian revolution in which there was “a competition”, and that it “institutionalized” competition in the presidential elections, and introduced new debate on the issues of religion, economics and other foreign and domestic policies. But he believed those elections were an “exception” and doubtful of their repetition, "though he did not explain why", according to al-Monitor.