The first plane carrying 100 Kenyans evacuated from South Sudan after fresh violence landed at the JKIA in Nairobi at about 2.30pm on Saturday.
Six more planes are expected today, Foreign Affairs PS Monica Juma said and urged members of the public not to travel to South Sudan.
Fifteen Kenyan truck drivers and six from Uganda were shot dead near Jebel town in South Sudan last Saturday.
They were caught in a crossfire on their way from Juba, said the Kenya Long Distance Truck Drivers and Allied Workers Union.
Secretary general Nicholas Mbugua said eight others were still missing but that Kenyan and South Sudan authorities were carrying out searches.
Kenya Airways had suspended flights to Juba, where it flies three times daily, but these were restored after a ceasefire.
At least 300 people have been killed and more than 42,000 displaced following the violence that erupted last Thursday between fighters allied to President Salva Kiir and First Vice President Riek Machar.
Uganda's army began evacuating its citizens on Thursday after the fighting that has plunged the nation into its worst crisis since the end of a two-year civil war.
Other countries including Germany, the UK, Italy, Japan and India have also taken their people out of the country.
US President Barack Obama announced 47 troops were being sent to protect the US embassy and its staff.