"I congratulate Prime Minister Haider al-Abadi and the Iraqi people for their progress in freeing the city of Fallujah from the grip of IS," Carter said in a statement.
Carter said the US and its coalition partners are proud to have supported Iraqi security forces under Al-Abadi's command in this important operation.
This he described as "another milestone" in efforts to accelerate IS' defeat.
"The operation in Fallujah has been a significant challenge for the ISF and for the coalition," he said.
"It is also essential to complete the investigations the government of Iraq has launched to address alleged abuses of civilians. Despite the hard work still to do, the clearing of Fallujah will make the people of Iraq safer and bring us all one step closer to dealing IS a lasting defeat," Carter said.