In the city centre, mourners clutching portraits of Raisi gathered on Wednesday in and around the University of Tehran, where Supreme Leader Ayatollah Ali Khamenei led the prayers.
Flanked by top officials, Khamenei said prayers over the coffins of the dead, who also included Foreign Minister Hossein Amirabdollahian.
Raisi’s helicopter crashed into a fog-shrouded mountainside in northwestern Iran on Sunday as he headed back to the city of Tabriz after attending a ceremony on the border with Azerbaijan.
A huge search and rescue operation was launched, involving help from Turkey, Russia and the European Union. State television announced Raisi’s death early on Monday.
Raisi, who was widely expected to succeed Khamenei as supreme leader, was 63.
In Tehran, huge banners went up hailing the late president while others bade “farewell to the servant of the disadvantaged”.
Tehran residents received phone messages urging them to “attend the funeral of the martyr of service”.
Funeral rites for Raisi and his entourage began on Tuesday with processions through Tabriz and the Shia clerical centre of Qom drawing tens of thousands of black-clad mourners.
From Tehran, the bodies will be taken to Iran’s second city of Mashhad, Raisi’s hometown in the northeast, where he will be buried after funeral rites at the Imam Reza shrine.
After his death, global allies Russia and China sent their condolences, as did NATO, while the UN Security Council observed a minute’s silence.