Machar, who used a United Nations chartered aircraft landed at Juba International Airport at 3:45 PM.
Machar and Kiir are expected to form a Transitional Government of National Unity.
Machar was supposed to return to Juba on April 18, but delayed several times over disagreement on the number of soldiers and weapons he brings with him to Juba.
On Monday, his army chief of staff arrived in Juba with 195 soldiers and 20 PKM machine guns and 20 rocket grenade launchers.
Machar’s rebellion against the government started in December 2013 – four months after he was dismissed as Vice President by Kiir.
Kiir accused Machar and his followers of a coup attempt, but Machar denied. Violence escalated along ethnic lines, killing tens of thousands and displacing millions.
After months of mediation, negotiation and pressure from the international community, the two parties signed a fragile peace agreement in August 2014.
Machar’s return and the formation of the Government of National Unity is seen by many as leap toward peace in South Sudan.