South Sudan army chief General James Ajongo died in Cairo following a short illness, government spokesman Michael Makuei Lueth said.
“It is with a heavy heart I announce the untimely death of General James Ajongo Madut, SPLA army’s chief of defence force,” Lueth said.
Ajongo joined the Sudan People’s Liberation Army, the formal name of the South Sudanese military, in 1983, when the SPLA was still a rebel group fighting for independence from Sudan.
He was appointed after his predecessor Paul Malong was sacked early last year amid resignations by generals who alleged abuses by the military and tribal bias in the army ranks.
Malong has since formed his own organisation to challenge President Salva Kiir, accusing him of looting the country’s resources and turning it into a failed state.
South Sudan, which obtained independence from Sudan in 2011 and is the world’s youngest nation, has been mired in civil war since 2013 when Kiir fired his deputy Riek Machar.
Tens of thousands of people have been killed in war often fought along ethnic lines and much of the nation has faced dire food shortages.