South Sudan President Salva Kiir has relieved Managing Director, James Thelweng Mathiang Rok, of his duties from national oil company Nilepet, Reuters said.
Since February Rok has held the position, but has been replaced by new managing director Chol Deng Thon Abel.
The new nation as of 2011 has seven billion barrels of oil in proven reserves. But South Sudan has been mired in civil war since the end of 2013, less than two years after it gained independence from Sudan and autonomy over its petroleum reserves.
Oil accounts for almost 100% of the country's export revenue, but hard currency reserves have been slashed by a fall in oil prices and in output since war broke out.
This has fueled rampant inflation and fuel shortages are currently gripping the capital, in part due to lack of dollar reserves to buy imports and to flooding on the main road to Uganda, where fuel tankers from the Kenyan port of Mombasa make their way into the landlocked country.
The conflict has also forced nearly a third of the population of 12 million to flee the country, creating Africa's biggest refugee crisis since the 1994 Rwandan genocide.