Machar, who under the terms of the peace deal is to be reinstated as vice president, had not set foot in the city since he fled in July 2016 under a hail of gunfire when an earlier peace accord collapsed.
The rebel chief arrived at Juba airport at 9:30am (0630 GMT) and was welcomed by President Salva Kiir, Machar's former ally turned bitter enemy.
The two are to join regional leaders at the ceremony later Wednesday to publicly welcome the most recent peace agreement, signed in the Ethiopian capital Addis Ababa in September.
It was not immediately clear if Machar would remain in Juba after the ceremony, as his aides have expressed concerns over his safety in the city.
South Sudan's civil war began in December 2013 when Kiir accused Machar -- then his deputy -- of plotting a coup.
The conflict split the country along ethnic lines and seen mass rape, the forced recruitment of child soldiers and attacks on civilians. It has caused one of the world's deepest humanitarian crises.
Several ceasefires and peace agreements have so far failed to end the fighting that has killed an estimated 380,000 people, uprooted a third of the population, forced nearly two-and-a-half million into exile as refugees and triggered bouts of deadly famine.
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