This was announced by the civil aviation authority.
In March this year, the government suspended flight operations as a precautionary measure to prevent the spread of COVID-19.
According to the BBC, the Director-General of Juba International Airport, Kur Kuol, said Ethiopian Airlines had been the first non-domestic carrier to land in the airport. The airline is now operating daily flights from Addis Ababa, Ethiopia's capital.
A Sudanese cargo and passenger airline, Badr Airlines, has also resumed operations.
Meanwhile, United Arab Emirates airline FlyDubai will resume regular flights to Juba on Friday.
All passengers who arrive in the country will have to isolate themselves for 14 days and observe all health regulations.
“Our air space is now open, we have no restrictions on the airlines. But whoever is coming into the country from outside, whether he or she is a foreigner or a South Sudanese national, must provide a health certificate and must self-quarantine for 14 days before engaging with the public while in the country,” Mr Kuol said.