The visit is Machar's first he fled into hiding when fighting broke out in Juba in mid-December.
Machar’s spokesman, James Gatdet Dak, said the opposition leader will "discuss issues pertaining to the promotion of the peace process."
The peace talks for South Sudan, led by the Intergovernmental Authority on Development (IGAD), have been put on hold several times since they began in January.
Machar and President Salva Kiir met earlier this month when the talks were in session, and signed a cessation of hostilities agreement, which was violated within days of their signing it.
Dak said it was unclear how long Machar will remain in Nairobi.
"It will depend on the issues to be discussed. He may be here for a few days or maybe for a week,” he said.
South Sudan Ministry of Foreign Affairs spokesman Mawien Makol Arik said the government has no control over Machar, so he is free to move as he wants.
He said he hopes that Machar's interlocutors will encourage him to adhere to the peace deal and not attack government forces or civilians who support the government.
Philip Aleu contributed to this report from Juba.
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