Mullen heads a council of senior admirals and generals from the four US military branches that advises US President George W. Bush on military policy.
"I can confirm Admiral Mullen arrived in Baghdad Saturday to meet with commanders and Iraqi officials," read a statement from the US-led forces.
The visit coincides with the arrival in Baghdad of Iranian President Mahmoud Ahmadinejad, the first ever visit of an Iranian president to Iraq.
Bush on Saturday warned Ahmadinejad to "stop exporting terror," and urged Tehran to stop arming anti-US militias.
The United States has accused Iran of supplying Iraqi insurgents with bombs used to attack US soldiers and is increasingly concerned over Tehran’s influence in the Shiite-majority country.
The United States currently has 158,000 troops stationed in Iraq.