Speaking amid a summit to highlight the plight of youngsters, the Christian organisation said the international community must do more.
Judy Moore, West Nile Refugee Response Director, said: "If governments, humanitarian and development agencies and business leaders come together we can help children who have lost everything rebuild their lives and build a brighter future."
Some 1.9 million people have fled a civil war in South Sudan which broke out in 2013. Approximately 60 per cent of the 900,000 South Sudanese refugees in Uganda are children.
Judy Moore went on to say: "Many vulnerable children I have met in Bidi Bidi have been terrified by what they have seen and are grieving the loss of parents and siblings. They need protection and support."
A meeting between the United Nations and Uganda's President Yoweri Museveni at the Uganda Solidarity Summit on Friday was also trying to help raise £6.3 billion to improve to the wave of South Sudanese refugees.
So far, funding has been secured for just 16 per cent of the international aid response.
Judy Moore described the summit as "an opportunity to prevent the world's fastest growing refugee crisis becoming one where refugees face long-term need."
Some 2,000 people are crossing the border from South Sudan in Uganda. World Vision says it is registering 100 unaccompanied children every day at the Bidi Bidi settlement.
The charity says children arriving in Uganda have already been provided with "child-friendly spaces" for learning and play, and psycho-social support.
Click here to listen to Premier speaking with World Vision's Kathryn Taetzsch in Uganda: