Cerkez is expected to return aboard a regular Croatia Airlines flight from the Netherlands via Zagreb to Split where his family lives.
Cerkez has been in detention since 6 October 1997 when he surrendered voluntarily together with another Bosnian Croat leader, Dario Kordic.
In February 2001 the tribunal sentenced Cerkez and Kordic to 15 and 25 years in prison respectively for war crimes committed in the Lasva valley in the 1992-1994 period.
On Thursday, the tribunal released a statement reading that the Appeals Chamber ordered the immediate release of Cerkez from the detention centre.