Gen Abdel Fattah Al Burhan, also chairman of Sudan's ruling Sovereignty Council, will discuss the conflict in his country with South Sudanese President Salva Kiir, the council said.
Mr Kiir received Gen Al Burhan at the airport in Juba.
Gen Al Burhan is being accompanied by acting foreign minister Ali Al Sadiq and military officers including Gen Ahmed Ibrahim Mufadel, leader of the General Intelligence Authority, the council said.
Gen Al Burhan and his delegation departed from Port Sudan airport, Sudan News Agency reported.
“We in Sudan feel that South Sudan is the best country to meditate the conflict in Sudan, because we have been one country for so long and we know each other, we know the problems and we know our needs,” Mr Al Sadiq said in a statement posted on Facebook.
The mainly Christian South Sudan seceded in 2011 after two decades of civil war with the mainly Muslim and Arabised north.
More than a million Sudanese have fled the violence in their country, crossing the borders to countries including South Sudan, Chad and Egypt.
Nearly five million have been displaced by the fighting, mainly centred in Khartoum and the western Darfur region.
Tensions between the Sudanese military and the paramilitary Rapid Support Forces, led by Gen Mohamed Dagalo, erupted into open fighting in Khartoum in mid-April, before spreading to other parts of the country.
Gen Al Burhan travelled from Port Sudan to Egypt last week for talks with President Abdel Fattah El Sisi in the coastal city of New Alamein. It was the Sudanese army chief's first trip abroad since the war began.
Egypt and South Sudan neighbour Sudan.
Gen Al Burhan left Khartoum about two weeks ago for the first time since the war with the RSF began in April.
The RSF has repeatedly said he was besieged in the section of the armed forces' headquarters held by the army.
Gen Al Burhan never publicly explained how he left the headquarters, saying only that his exit was not negotiated with the RSF.
He has since visited an army-held airbase near the Sudanese capital and the city of Atbara farther north.
Since leaving Khartoum, Gen Al Burhan has vowed to have no dealings with the RSF and to continue to fight against the group. He has also warned that Sudan could break up if the war is not decided quickly.