Mathieu Ngudjolo was the head of the Front of Nationalists and Integrationists (FPI) militia during conflict in northeast Ituri Province that grew out Congo's 1998-2003 war.
He was arrested by Congolese authorities on Wednesday and handed over to ICC custody.
"He left very early this morning ... escorted by a security detail from the ICC," Paul Madidi, the court's spokesman in Democratic Republic of Congo's capital Kinshasa, told Reuters.
Ngudjolo is the third Ituri warlord to be transferred to the ICC in the last year.
Another Congolese militia chief, Thomas Lubanga, was taken into custody by the court last year and his trial is due to start on March 31. He is accused of recruiting children under the age of 15 to kill members of another ethnic group.
The ICC is also in the process of prosecuting Germain Katanga, another Ituri ex-militia leader who is accused of murder, sexual slavery and using child soldiers.