In his first visit to the region, al-Bashir, who arrived in South Sudan on Friday, stressed a call for restoration of good neighborly cooperation and brotherly ties with South Sudan, which gained independence in 2011. His visit raised hopes the two adversaries may be edging toward establishing peaceful co-existence.
The neighbors agreed in March to resume cross-border oil flows and take steps to defuse the tension that has plagued them since South Sudan's independence in July 2011 following a treaty which ended decades of civil war.
Bashir landed at Juba airport with a 65-strong delegation and was met by South Sudan's Salva Kiir.
South Sudan's secession left unresolved a long list of disputes over territory and how much the landlocked south should pay to export its oil through Sudan.
The new African country shut down its entire oil output of 350,000 barrels a day in January last year at the height of the dispute over pipeline fees - a closure that had a devastating effect on both struggling economies.
The two sides subsequently agreed to restart oil shipments, grant each other’s citizens residency, increase border trade and encourage close cooperation between their central banks.
Last week, South Sudan re-launched oil production with the first oil cargo expected to reach Sudan's Red Sea export terminal at Port Sudan by the end of May.
Both nations also withdrew their troops from border areas as agreed in a deal brokered by the African Union in September.
Bashir last visited Juba on July 9, 2011, to attend the ceremony marking South Sudan's formal separation.