This is the first of several shipments scheduled to arrive in the country over the coming months through the global partnership Covax.
About 732,000 doses of vaccines are expected by June. The country plans to eventually vaccinate 20% of its population.
The health ministry and the World Health Organization (WHO) have said health workers will be given priority for first doses.
It will also target persons aged 65 years and older, who are likely to be at higher risk of getting severe Covid and dying.
“As a daughter of South Sudan, I am a happier woman today and I really thank God that at last we got vaccines for our people,” Health Minister Elizabeth Achuei Yol told reporters.
She assured the people of the safety of the vaccine.
“I am here surely to tell you that this vaccine is safe for you. So, please stay calm, and when your time comes for taking the vaccine, come so that you can be protected,” she said.
South Sudan has 9,969 confirmed cases of Covid-19 and 107 deaths, according to the country’s health ministry.