Yesterday, the capital was festooned with the flags of his Sudan People's Liberation Movement (SPLM) and thousands of his supporters waited in the hot sun to make sure they did not miss his arrival.
Mr Garang's journey to Khartoum from Rumbek, the southern town that was the SPLM stronghold for many years, will mark the formal end of a 21-year civil war that killed more than two million people and devastated south Sudan. He becomes the first Christian to hold such a senior position in Sudan's Islamic government and many hope his appointment will encourage Sudan's autocratic regime to modernise.
Last month, the government freed high-profile political prisoners including the opposition leader Hassan al-Turabi and tomorrow it will lift a 16-year state of emergency declared across most of the country.
"Garang's going to unite the whole of Sudan and he's going to bring peace in the whole of Sudan," Mariam Oketch, a southerner who fled the fighting to live in Khartoum, told reporters.
Today's celebrations will not affect Darfur in western Sudan, where 180,000 people have died and two million have lost their homes in attacks by government forces and the janjaweed militia. Mr Garang said he hopes his peace deal can be used as a blueprint for a similar one in Darfur but the rebel groups there are reluctant to accept his authority.
This will be the second time Mr Garang has worked with the government. In the early 1980s, he was sent as an army officer to suppress a mutiny in the south. Instead of ending the uprising, he took charge of the rebel troops and in 1983 launched a civil war to win greater equality for southern Sudan. His main aim was to ensure the mainly Christian southern Sudanese kept control of the oil that was discovered on their lands in 1978.
During the war, south Sudan enjoyed a great deal of support from American churches, and US pressure finally forced both sides to sign a peace deal in Nairobi this year. The peace deal Mr Garang signed with the Khartoum government in January achieved most of his goals. It set up wealth- and power-sharing agreements between the north and south and exempts the mainly Christian south from sharia, Islamic law, which is practised in Khartoum.
This week, the Sudanese parliament approved an interim constitution paving the way for Mr Garang's appointment. In six years, south Sudan will vote on whether to secede from the rest of the country. Mr Garang wants Sudan to remain unified but most south Sudanese want separation.