The 133 returnees touched down at Juba International airport on Thursday morning.
They were received at the airport by the Undersecretary in the Ministry of Humanitarian Affairs, Clement Dominic.
Dominic told Radio Miraya that another two flights are expected on the 18th and the 23rd of this month to complete the airlifting of the estimated 300 refugees still in Israel.
Speaking to Radio Miraya, some of the returning citizens expressed happiness to be home again and take part in building the new nation.
More than 1,500 South Sudanese who were living in Israel are returning home as part of an operation by the Israeli government to deport illegal migrants.