Government officials in Juba were not available to comment.
NRC, which has operated in South Sudan since 2004 and provides services such as food distribution and construction of emergency shelters in remote areas, said no reason was given for the action.
"The expulsion of our Country Director is a serious setback to our humanitarian work for civilians in dire need of support," NRC's Secretary General Jan Egeland said in a stateement.
"To undermine our relief to vulnerable citizens' is an affront to the international humanitarian community in South Sudan," he added.
NRC, which did not disclose the name or nationality of its director, urged the government to reverse its decision.
South Sudan has been wracked by violence since a political rift between its President Salva Kiir, an ethnic Dinka, and his former deputy Riek Machar, a Nuer, led to civil war in 2013 that has often followed ethnic lines.
The pair signed a peace agreement last year but fighting has continued and Machar fled the country in July.
Aid agencies say violence has displaced more than three million people, a third of whom have sought refuge in neighbouring countries.
(reporting by Denis Dumo,; writing by Aaron Maasho, editing by Angus MacSwan)
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