Al-Ha'iri returned briefly to Iraq after the fall of the Hussein regime in 2003. In April of that year, Muqtada al-Sadr asked al-Ha'iri to serve as his adviser and to head the Al-Najaf Hawzah (seminary).

Al-Ha'iri has been described in the media as representing "the point of convergence" between the al-Sadr current, the Al-Da'wah, and the Supreme Council for the Islamic Revolution in Iraq (SCIRI).

He reportedly also has strong relations with the religious authorities in Iraq, Iran, and Lebanon. Al-Ha'iri is staunchly anti-American and issued a fatwa in May 2003 saying it was lawful for Muslims to kill senior Ba'ath party officials.

Appointed Muqtada al-Sadr as his representative in Iraq. Many Shi'a in Al-Najaf don't recognize his authority over Iraqis.