The End of the Velayat-e Faqih System in Iran Following the Death of Ali Khamenei

On March 9, 2026, the Assembly of Experts—composed of Shiite clerics tasked under Iranian law with selecting the Supreme Leader (Vali-ye Faqih)—officially announced that Mojtaba Khamenei had been unanimously elected by those participating in the vote as the Third Supreme Leader of the Islamic Republic of Iran. It was reported in the media that only 59 out of the 88 members of the Assembly of Experts participated in the election, while the remaining members were not informed. Although the required two-thirds majority for the election was achieved, the manner and timing of the vote created the impression of a hasty and opaque process.

The selection of the Third Supreme Leader provided important indications regarding whether the doctrine of Velayat-e Faqih would be upheld, whether the system itself would continue, and how the Islamic Republic of Iran would proceed.

In our article titled “Iranian Elections in Terms of Preparation for the Next Supreme Leader Selection,” published on March 19, 2024, the 12th parliamentary elections held on March 1, 2024, along with the elections for the 6th Assembly of Experts—responsible for selecting, supervising, and dismissing the Supreme Leader—were evaluated, and attention was drawn to the potential role of the Assembly of Experts in the selection of the Third Supreme Leader.[i]

In that article, it was predicted that one of two candidates would be selected, namely the then-President Ebrahim Raisi or Mojtaba Khamenei, the son of Ali Khamenei. One of the prospective candidates, President Ebrahim Raisi, died in a suspicious helicopter crash on May 19, 2024—two months after the elections. At the time, some interpreted this incident as part of an internal power struggle aimed at eliminating one of the potential successors to the Supreme Leader.

As a result, Mojtaba Khamenei—despite being considered unlikely by many—continued as the strongest candidate, and the Assembly of Experts ultimately announced that he had been selected to replace his father, the Second Supreme Leader Ali Khamenei, who was killed in the U.S.-Israeli attacks on February 28.

How Was the System of Selecting the Vali-ye Faqih Constructed?

It is highly probable that the identity of the Third Supreme Leader had been determined by the establishment prior to the March 1, 2024 elections. According to the Iranian Constitution, candidates wishing to run for the 88-member Assembly of Experts must first receive approval from the 12-member Guardian Council (Anayasa Koruyucular Konseyi, AKK). Of these 12 members, six clerics are appointed directly by the Supreme Leader, while the remaining six jurists are selected by the head of the judiciary—who is himself appointed by the Supreme Leader. Thus, the system was engineered in such a way that all pathways ultimately led back to Ali Khamenei through a complex mechanism of electoral design. The Guardian Council selected candidates for the March 1 elections from among those who would act in accordance with the directives of the establishment. Consequently, Ali Khamenei, through the Assembly of Experts formed by the Guardian Council, effectively determined his successor—his son Mojtaba Khamenei—indirectly, without issuing a formal designation.

In our 2024 article, we stated: “The identity of the third Supreme Leader will be determined by the preference of the Islamic Revolutionary Guard Corps (IRGC), which has gained sufficient power within the Assembly of Experts. Naturally, the IRGC will prefer a figure they can control—someone who will not undermine their existing power and influence within the system, who lacks an independent support base, and who will not challenge them.”

At that time, two potential candidates were mentioned: then-President Ebrahim Raisi and Mojtaba Khamenei. It was widely expected that Raisi’s rise—from being appointed as head of the judiciary by Ali Khamenei to becoming President—would culminate in his selection as Supreme Leader. However, Raisi’s death in a helicopter crash removed him from the race.

In the same article, we also pointed out that the power of the Third Supreme Leader would likely be limited and that the Velayat-e Faqih system would come under the control of the IRGC, which had become the dominant center of power:

“With the selection of the Third Supreme Leader, the position of Vali-ye Amr-e Mominin, which according to the Iranian Constitution represents the Prophet and the Twelve Infallible Imams, may in practice become accountable to the IRGC.”

Mojtaba Khamenei, who was selected as the Third Supreme Leader at the age of 56, is known to have maintained close ties with key security institutions—particularly the Office of the Supreme Leader and the Islamic Revolutionary Guard Corps—since the age of 17. These relationships have also played a significant role in facilitating communication between the leadership and the IRGC.

Since 2018, individuals employed in public institutions in Iran have been categorized as either “loyal to the Revolution” or “not loyal.” Those perceived as distant from the IRGC were purged on the grounds of disloyalty. During the tenure of Ali Khamenei, the IRGC consolidated its power by appointing its affiliates to key positions within the legislative, executive, and supervisory bodies, thereby becoming the true owner of the establishment.

Following the announcement of his leadership on March 9, 2026, it was also reported that Mojtaba Khamenei had been seriously injured in the same attack that killed his father. This further indicates that the establishment—now under the control of the IRGC—had pre-selected Mojtaba Khamenei as Supreme Leader to ensure continuity of the system.

In our previous analysis, we also predicted: “Ongoing economic difficulties due to sanctions, internal unrest, declining trust in the system, fears of ethnic fragmentation, and the exclusion of opposition groups from politics and bureaucracy all indicate that the already existing security-oriented governance structure in Iran will become even stronger, while spaces for freedom will continue to shrink.”

In light of the U.S.-Israeli attacks against Iran that began on February 28, it is evident that the role of the IRGC has expanded and that it has become the absolute authority within the system. During Mojtaba Khamenei’s tenure as Vali-ye Faqih, it is expected that the influence of the IRGC will further increase, while both the presidency and the religious leadership may become largely symbolic in the face of this dominant power structure.

Theological Debates over the Velayat-e Faqih System Will Intensify

According to Shiite belief, the Velayat-e Faqih system, designed to represent the deputyship of the Awaited Mahdi, has now evolved toward a model in which the Vali-ye Faqih becomes the deputy of the Revolutionary Guards. This transformation will bring about very serious theological debates within the Shiite world.

In the unique state model of the Islamic Republic of Iran, based on the doctrine of Velayat-e Faqih, also described as “theocratic authoritarianism,” the source of political authority is Twelver Ja‘fari Shiite jurisprudence. This authority is exercised by the religious leadership, the Vali-ye Faqih/Supreme Leader, who is regarded as the deputy of the Awaited Mahdi during his occultation and is elected for life by the Assembly of Experts.

The doctrine of Velayat-e Faqih, developed by Ayatollah Khomeini, was institutionalized in the Iranian Constitution, and the “Vali-ye Faqih” represents the Prophet and the Twelve Infallible Imams. The Office of the Supreme Leader, standing above all powers including the legislative, executive, and judicial branches, is the highest authority of the state. As Vali-ye Amr-e Mominin, during the period of the Hidden Imam, he is not only the religious leader and ruler of the Islamic Republic, but of the entire ummah.

From the very beginning, the doctrine of Velayat-e Faqih faced serious objections from Shiite scholars. Shiite scholarly circles institutionalized in Najaf from the 11th century onward did not consider it permissible to establish a Shiite state before the emergence of the Mahdi. Based on the belief that a Shiite state could only be established and governed by the infallible Imams, they regarded the idea of a state claiming to act as the deputy of the Mahdi as invalid, remained distant from state-building efforts, and even declared such a state to be taghuti.

Instead of establishing a state, the system required all Shiites, both inside and outside the seminary sphere, to follow Shiite sources of emulation known as Ayatollah al-Uzma through taqlid. This system continued for centuries without the need for a state.

The concept of Velayat-e Faqih was first articulated in Iran in the 19th century by the Shiite marja Ahmad Naraqi. After 1965, it was developed by Ruhollah Khomeini and transformed into a doctrine. In 1970, Khomeini’s views on Velayat-e Faqih were compiled into a book under the title Hukumat-e Islami, Islamic Government, and published in Najaf.

Following the Iranian Islamic Revolution, the Islamic Republic of Iran was declared on April 1, 1979. With Articles 5, 109, and 110 of the Constitution, approved by referendum on December 3, 1979, the Velayat-e Faqih system was adopted, and it was determined that Khomeini would represent the Office of the Supreme Leader.

Many maraji‘ of the period, including Ayatollah al-Uzma Khoei, Ayatollah al-Uzma Shariatmadari, and Ayatollah al-Uzma Montazeri, opposed this doctrine on the grounds that it would usurp the position of the Mahdi.

The Velayat-e Faqih system, which began to institutionalize after 1980, created a conflict between the Supreme Leadership and the institution of marja‘iyya through an authoritarian state model based on the absolute authority of the Vali-ye Faqih. One of the most significant theoretical objections to the system came from Muhammad Shirazi. He argued that placing a single marja‘ in this position would lead to dictatorship and contradict the plural marja‘iyya system in Shiism. Accordingly, he advocated the theory of Velayat-e Fuqaha, the Guardianship of Jurists.

Maraji‘ and ayatollahs who defended the traditional autonomy of the marja‘iyya institution and religious seminaries from the state, and who opposed their integration into the state order, as well as those who held different understandings of Shiite jurisprudence, were treated as threats to the new state; they were punished, silenced, and excluded.

The words of Ayatollah Sayyid Ali Husayni Sistani, the marja‘ of the Najaf seminary, regarding the Iranian state structure clearly summarized the relationship between the Supreme Leader and the mujtahids in Iran: “Muhammad Beheshti prepared the constitution in such a way that only matters of ghusl and wudu were left to the sources of emulation. The rest was handed over to the state.”

Ayatollah Khomeini, benefiting from the atmosphere created by the Iran-Iraq War of 1980-1988, suppressed the opposition, rendered the Qom clergy passive, and dominated the new regime by placing his students in critical positions, such as Ali Khamenei as president and Hashemi Rafsanjani as speaker of parliament. Thus, he gained the opportunity to implement his own theory of Velayat-e Faqih by directly managing the state, domestic politics, and foreign policy.

Both the First Supreme Leader, Ruhollah Khomeini, and Ali Khamenei, who was selected as the Second Supreme Leader from 1989 onward, established absolute authority over the state through unelected and parallel institutions such as the Guardian Council and the Expediency Discernment Council, and built a closed system against those who were not loyal to the Supreme Leader. The Islamic Revolutionary Guard Corps, the Basij Militia, the Ministry of Intelligence, and the Revolutionary Courts reflected the power of the Supreme Leaders on the ground through harsh and severe practices.

There were also deviations from the doctrine during the implementation of the system. The most important of these was the removal, in 1989 on Khomeini’s instruction, of the constitutional requirement that the person who would assume the Office of the Supreme Leader must be a marja‘ al-taqlid/Ayatollah al-Uzma. The elderly and ill Khomeini had this amendment made in order to pave the way for his student Ali Khamenei to become Supreme Leader after him, because Khamenei was not a marja‘ al-taqlid and had not even yet reached the rank of ayatollah.

Ali Khamenei, who was selected as the Second Supreme Leader in 1989 after Khomeini’s death, did not possess the broad charisma and religious authority that Khomeini had. Khamenei compensated for this weakness and deficiency by relying on the Revolutionary Guards, forming a mutually reinforcing coalition with them.

Through the Supreme Leader-Revolutionary Guards coalition, a large part of the economy came under the control of the Islamic Revolutionary Guard Corps and its consortium of affiliated companies, such as Khatam al-Anbiya, as well as religious foundations, the bonyads. Due to widespread corruption among those controlling the administration and social inequality, the system lost its credibility. Over time, those who raised legitimate complaints about unjust practices, poverty, and unemployment, and those who participated in protests, were accused of treason, hostility toward the state, and being agents of foreign powers. Demands for freedom of the press and freedom of expression were suppressed as sedition through the intervention of the Revolutionary Guards and militia forces.

Conclusion

In our view, the 46-year period of Velayat-e Faqih, carried out between December 3, 1979, and February 28, 2026, under the leadership of the First Supreme Leader Ruhollah Khomeini (1979-1989) and the Second Supreme Leader Ali Khamenei (1989-2026), has effectively come to an end. The period of Mojtaba Khamenei, selected as the Third Vali-ye Faqih, will most likely be a period in which the religious leadership submits to the dominant center of power and the Supreme Leader performs his duties under the tutelage of the Revolutionary Guards.

Some time after the end of the U.S.-Israeli war against Iran, the 46-year Velayat-e Faqih period, which failed both in governing society domestically and in foreign policy, will be subjected to deep criticism and questioning in Shiite seminaries, especially in Qom.

Among the Iranian people, obedience to the authority of the Vali-ye Faqih has already fallen to extremely low levels. Despite Vali-ye Faqih Ali Khamenei’s fatwas stating that voting by those qualified to participate in elections is a religious, Islamic, and divine duty; that voting is fard al-ayn, an individual obligation incumbent upon everyone; and that casting a blank ballot is haram, turnout in the general election held on March 1, 2024, remained at 41 percent. In other words, 60 percent of the people disregarded the Supreme Leader’s fatwas. Both in this election and in the presidential election held on July 7 of the same year, more than half of the votes were cast for reformist candidates, revealing that trust in and loyalty to the Supreme Leader had fallen to around 20 percent nationwide.

However, participation in the March 1979 referendum on the transition to the Islamic Republic was 89 percent, and the proposal was approved with 98.2 percent voting in favor. The decline in support for the regime today is the result of unjust and hopelessly poor governance during the 46-year period of Velayat-e Faqih, which came to power with the claim of “establishing justice.”

It appears that the 900-year-old traditional institution of marja‘iyya, which the Khomeini-Khamenei leadership attempted to eliminate, and the 46-year-old Islamic Republic of Iran will undergo a theological reckoning, and the institution of marja‘iyya may find the opportunity to revive.

According to the Iranian Constitution, the Supreme Leader is not only the religious leader and ruler of the Islamic Republic, but of the entire ummah. However, the institution of Velayat-e Faqih has destroyed this claim through its rigid sectarian identity. The Revolutionary Guards, directly subordinate to the Supreme Leader, attempted to export the revolution to the Sunni world and, through the “Axis of Resistance” it established, caused bloody conflicts in many countries, particularly Lebanon, Iraq, Syria, and Yemen, yet failed to achieve success. In the new period, the erosion of the institution of Velayat-e Faqih and the Supreme Leader’s sharing of his religious authority with centers of power will also lead Shiites living outside Iran to reduce their attachment to Velayat-e Faqih and will accelerate the tendency of Shiites exhausted by the “Axis of Resistance” to turn toward the maraji‘ al-taqlid in both the Qom and Najaf seminaries. As a result, the strategic advantages that Iran established over regional countries through the institution of Velayat-e Faqih will rapidly disappear.

Considering the religious reckoning that will be added to its current political, social, and economic crises, difficult days await Iran. It does not appear possible for the Revolutionary Guards to stabilize Iran through power politics.

Footnote:

[i] Iranian Elections in Terms of Preparation for the Next Supreme Leader Selection
https://www.sde.org.tr/sinan-tavukcu/genel/bir-sonraki-rehber-secimi-ne-hazirlik-acisindan-iran-secimleri-kose-yazisi-53588