The Green Zone houses parliament, government buildings and many foreign embassies.
Three mortar shells landed inside Baghdad's heavily fortified Green Zone just after midnight local time on Friday, the Iraqi military said in a statement.
The mortars landed on an "abandoned lot," resulting in "no casualties or physical damage," the statement said.
A security source inside the Green Zone said the mortars landed near the Egyptian embassy.
No group immediately claimed responsibility for the attack, which comes after days of intensifying protests in Iraq's southern oil hub city of Basra.
Hundreds of protesters, angry over the neglect of their city's collapsing infrastructure, took to the streets for a fourth day on Thursday, setting fire to political party offices and government buildings.
The mortar attack is the first such one in several years on the Green Zone, which houses parliament, government buildings and many foreign embassies.
In May 2016, three mortars landed near the Green Zone. Anti-corruption protesters, led by populist Shia cleric Moqtada al Sadr, breached the Green Zone twice that year, storming parliament and the cabinet office.
Sadr is now vying to form Iraq's ruling coalition in an alliance with incumbent Prime Minister Haider al Abadi, his electoral bloc having come first in May's national election.
The Green Zone was regularly targeted by mortars during the US occupation of Iraq that ended in 2011.