Omar al-Bashir sat down with Salva Kiir during an African Union summit in Ethiopia's capital Addis Ababa.
South Sudan only became independent from the north at the end of 2011 and numerous issues remain unresolved between the two countries.
A United Nations deadline for them to settle the dispute is set for 2 August.
Among other issues, their border has not been finalised and there are disagreements over oilfields, transport payments and divisions of the national debt.
No information has been released about what the two men spoke about during their meeting in Addis Ababa, but they shook hands publicly for the first time at the end of it.
The last official talks between Presidents Kiir and Bashir were at the previous AU summit in January.
At this summit, AU delegates urged the governments in Khartoum and Juba to settle their differences on oil and border demarcation before the UN's deadline.
The UN introduced its three-month deadline after cross-border clashes centred on the oil-rich region of Heglig brought Sudan and South Sudan close to all-out war in April.
South Sudan's independence in July 2011 was supposed to herald the end of more than 50 years of bitter conflict between the two Sudans, but tensions have lingered.
The BBC's Risto Pyykko in Addis Ababa says Saturday's meeting between the two leaders is unlikely to yield any immediate results, but at least shows the two countries are feeling the pressure to resolve their dispute.
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