Heatwaves are becoming increasingly common in the East African country, which is particularly vulnerable to climate change, but temperatures rarely exceed 40C.
"High temperatures of 41C-45C are expected this week," the ministries of education, health and environment said in a statement, adding that the heatwave was expected to last "at least two weeks".
"There are already cases of death related to excessive heat being reported," they added, without giving further details.
The government will close all schools from March 18 due to the "serious health hazards" posed to students.
"Parents are advised to stop their children from playing outdoors," the statement added, saying young children in particular should be monitored for signs of heatstroke.
Episodes of drought and increasingly extreme rainfall are adding to already difficult living conditions in South Sudan, which has been plagued by violence and economic instability since it declared independence from Sudan in 2011.
Scientists say that recurring heatwaves are a clear marker of global warming and that these heatwaves are set to become more frequent, longer and more intense.
One of the poorest countries in the world despite large oil reserves, South Sudan has spent almost half of its life as a nation at war, and has also endured persistent natural disasters, famine, economic collapse and communal conflict.
According to the UN, 80 percent of the country's estimated 11 million population will need humanitarian aid in 2024.
A power-sharing peace agreement was signed in 2018, but many of its provisions remain unfulfilled due to ongoing disputes.
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