The Pretoria High Court was due to decide whether he should be handed over to the International Criminal Court which charged him with the crimes.
According to a source, a news conference will be held in Sudan's capital upon his arrival.
The UN says that about 300,000 people in Sudan have died and more than two million have fled their homes since fighting began in 2003.
Government forces and allied Arab militias are accused of targeting black African civilians in the fight against the rebels.
