Alfred Yekatom arrived at the International Criminal Court (ICC) detention centre on Saturday.
The ICC alleges he was responsible for murder, torture, attacking civilians and using child fighters.
Mr Yekatom, known as "Rambo", led a Christian militia which formed after Muslim rebels seized power in 2013.
The group formed part of a band of mostly Christian militias, called the anti-Balaka, which rose up to counter the rebels.
The allegations against Mr Yekatom, which include war crimes, date back to late 2013 and early 2014.