Doors and windows shook in buildings in the city centre, but there was no immediate indication of what might have caused the latest explosion.
Firghters frequently fire mortars at the fortified Green Zone area in central Baghdad, which houses the Iraqi interim government and the US and other embassies, but Thursday's blast appeared to have detonated some distance from there.
The explosion was heard after fighters had attacked a US military convoy.
Aljazeera has learned that two explosions were heard on the road leading to Baghdad airport.
Clashes have also erupted between fighters and US forces in al-Jamia neighbourhood west of Baghdad, Aljazeera's sources said.
At least two car bombs have also exploded outside entrances to the Green Zone in the past week, killing at least nine people and wounding more than 20.
US and Iraqi authorities have said they expect a rise in anti-interim government attacks in the run-up to Iraq's election, scheduled for 30 January.
Campaigning for the poll officially got under way on Wednesday.