Bashir was greeted at Juba airport by South Sudan's Vice President James Wani Igga, before heading to the presidential palace for talks with his counterpart President Salva Kiir, an AFP correspondent said.
Bashir made no public comment upon arriving, although Khartoum yesterday reaffirmed Sudan's wish to see "a continuation of the political process aimed at finding a peaceful resolution to the conflict in South Sudan".
Sudan's foreign ministry also underlined Sudan's willingness "to offer everything in its power to ensure success of the initiative by IGAD", the East African regional bloc brokering the talks.
South Sudan won independence from Khartoum in 2011 after decades of war, but is dependent on Sudan for exporting its oil.