Zoellick, the highest-ranking US official to visit Sudan since former US secretary of state Colin Powell in July last year, is expected to fly on to Rumbek, the capital of the former rebel-held southern part of the country.
On Friday, the diplomat is also due to tour parts of the western area of Darfur, where tens of thousands have been killed and more than two million displaced by a two-year-old civil conflict and a dire humanitarian situation.
His visit comes two days after donor countries pledged 4.5 billion dollars in aid to help rebuild the devastated country, the largest in Africa, following the January 9 signing of a peace accord between Khartoum and the south.
Zoellick had warned at the donor conference in Oslo that the payment of the US administration's pledge would be conditioned on the Sudanese government's efforts to find a solution in Darfur.
The international community stepped up the pressure on Khartoum earlier this month when the United Nations passed a resolution referring Darfur war criminals to the international court in The Hague.
The Sudanese government and its proxy militias have been accused by the United States of committing atrocities in Darfur and failing to protect civilians.