Dr Rowan Williams is urging political leaders to do whatever is necessary to end the violence as soon as possible and is calling the Church to pray for an end to the conflict.
The South Sudanese civil war between government and opposition forces began in 2013 because of ethnic tensions before a ceasefire was declared in August 2015.
However fresh clashes have broken out this month with hundreds killed over reports of attacks against both President Salva Kiir and the opposition leader Riek Machar, who is also Vice-President.
The two called a ceasefire on July 11th but it's feared it will not hold.
Dr Williams, who is Chairman of Christian Aid which is providing humanitarian assistance in South Sudan, said: "The recent escalation of violent conflict in Juba since July 7 has caused yet more appalling suffering for the people of South Sudan who have over the past two and a half years endured the terrible consequences of a return to war and the bitter disappointment of hopes denied or deferred.
"It is - as so often - the poorest and most vulnerable who bear the brunt of the violence, who have lost lives, loved ones and homes. Thousands of people have been displaced by the recent violence. Many have sought refuge in church compounds across Juba, seeking safety and protection. These people are in need of urgent humanitarian assistance.
"As they did through decades of civil war, the churches once again stand as one of the few signs of hope, giving voice to the needs of the people of South Sudan... Their commitment to working for peace and reconciliation is as strong as ever."
