The flag hoisting ceremony further underlines the seriousness of Iran's call for avenging the death of the head of its elite Quds force, Qassim Suleimani, who was killed in a US airstrike earlier this week.
The hoisting of the flag took place Jamkaran Mosque — one of the primary significant mosques in the city of Qom, Iran — and telecast live on state TV.
Red flags in Shiite tradition symbolize both the blood spilled unjustly and serve as a call to avenge a person who is slain.
The flag, it is said, was hoisted on the shrine of Imam Hussain in Karbala after his martyrdom in the Battle of Karbala (680 AD) and has not been lowered till now keeping in line with the Shia tradition. The flag, the tradition dictates, will only be lowered once the death of Imam Hussain has been avenged.
It is the first time in the recent history that the flag has been hoisted at the Jamkaran mosque, Iran-based social media users commented.
Meanwhile, thousands of people descended on the streets of Iran calling for revenge. On Saturday, mourners chanting "America is the Great Satan" flooded the streets of the Iraqi capital Baghdad during the funeral procession of Suleimani and Abu Mahdi al-Muhandis, a senior Iraqi militia commander who was killed in the same strike.
The death of Suleimani has brought Iran face-to-face with its arch-rival, the United States, raising fears of an all-out war.
US President Donald Trump says he ordered the strike to prevent a conflict. His administration says Soleimani was plotting a series of attacks that endangered American troops and officials, without providing evidence.
Late on Saturday evening, a series of rockets launched in Baghdad fell inside or near the Green Zone, which houses government offices and foreign embassies, including the US Embassy.
On Sunday morning, the body of Soleimani arrived in Iran as President Trump issued fresh warnings directed at Tehran.
Trump later tweeted that the US had already "targeted 52 Iranian sites (representing the 52 American hostages taken by Iran many years ago), some at a very high level & important to Iran & the Iranian culture."
Trump did not identify the targets but added that they would be "HIT VERY FAST AND VERY HARD."