Mr Maliki, leading a large delegation including MPs and Iraq's national security advisory Muwaffak al-Rubaie for the two-day visit, went into talks with Ahmadinejad shortly after arrival.
President Ahmadinejad later vowed that Iran would help Iraq to provide "complete" security in the insurgency-ridden country, after talks with Mr Maliki.
"Iran will give its assistance to establish complete security in Iraq because Iraq's security is Iran's security," Mr Ahmadinejad said at a news conference with Mr Maliki.
"We had a good discussion with Mr Ahmadinejad. Even in security issues there is no barrier in the way of cooperation," the Iraqi prime minister said.
The prime minister will hold talks with the Islamic republic's supreme leader Ali Khamenei and influential former president Akbar Hashemi Rafsanjani.
The visit of the Shiite prime minister, who lived in Iran during the 1980s when Baghdad was at war with Tehran to escape persecution of his Dawa party, is his first since becoming prime minister.
The first visit by an Iraqi premier since the fall of Saddam Hussein was made by Mr Maliki's predecessor Ibrahim al-Jaafari in July 2005.
The two countries waged a war between 1980 and 1988 in which around one million people died but ties have warmed considerably since Saddam's fall, with Iran becoming a close ally of the Shiite-led Iraqi government.