The rivals, whose falling out in 2013 triggered a bloody civil war that has left almost 400,000 people dead and sparked a major humanitarian crisis, signed a peace deal in September last year that is meant to see them reunite once again in government.
The deadline for the formation of this government, in which Dr Machar will serve as first vice president, has already been delayed once and is now set for November 12.
However crucial technical steps contained within the agreement, such as creating a unified army and agreeing on the internal boundaries of states, have failed to make progress.
“The two will have a closed door meeting at the presidential palace today,” a spokesman for Machar’s party the SPLM-IO, Manawa Peter Gatkuot, said after the rebel leader’s arrival.
Dr Machar and Mr Kiir met in September in Juba, but failed to agree on the two issues of security and state boundaries.
When it won independence in 2011, the country was divided into 10 states but it has since been subdivided into 32, in what critics see as a gerrymandering of traditional boundaries by Kiir to shore up his power.
Dr Machar is also seeking assurances about his personal security before permanently returning to Juba, which he fled under a hail of gunfire when a previous peace deal collapsed in July 2016.
Efforts to get warring parties to canton their troops with a view towards forming a unified army — a key part of the peace deal — have made little progress.
Observers warn that the only way forward in the absence of progress on such sticky issues, is for Dr Machar and Mr Kiir to strike a new political deal that will enable them to move forward with the formation of a power-sharing government.