One of the rockets struck close to the American Embassy. The attack signals an end to an informal truce announced by Iran-backed militias in October.
Tehran accuses Trump and 35 others of involvement in the January drone strike that killed Gen. Qassem Soleimani in Baghdad.
The airstrikes came just hours after an attack killed and wounded American and British servicemen at a base north of Baghdad.
Hundreds of anti-government demonstrators flooded the streets of Baghdad and Iraq's southern provinces on Sunday.
The "million-man" march was called for by an influential Shiite cleric, though their numbers fell short of a million.
In the wake of a U.S. drone attack in Baghdad, Cardinal Louis Raphael Sako warned that “innocent people” will bear the cost of the heightened tensions.
Thousands marched through Baghdad on Saturday for Iran’s top general, who was killed in a U.S. airstrike.
His death is a potential turning point in the Middle East and is expected to draw severe retaliation from Iran.
Thousands of protesters gathered outside the American embassy in Baghdad on Tuesday to condemn U.S. air strikes.
The anti-government protest movement since Oct. 1 has accused the government of being corrupt and has also decried Iran’s growing influence in Iraqi state affairs.