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Mr Bashir and his southern counterpart, Salva Kiir, will discuss territorial disputes and border demarcation.
Also on the agenda is a recent deal on how much the South should pay for exporting its oil through Sudan.
The two countries came to the brink of war last year over unresolved disputes following South Sudan's secession.
However, there has been an easing of tension since they agreed to resume pumping oil last month.
Mutrif Siddiq, Khartoum's ambassador to the Southern capital Juba, said Mr Bashir would be warmly welcomed.
"President Bashir will discuss in his visit with Salva Kiir the relations between the two countries and how to develop and continue these relations for the benefit of both nations," he was quoted as saying by the official Suna news agency.
"The visit of President Bashir will receive a warm welcome in Juba from the government and the people of South Sudan," he added. (WIC)
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