The charity said since late August, 605,000 people have crossed the border from Myanmar into Bangladesh because of violence. As many as 60 per cent of these are children, and many have been separated from their parents.
Tanzina Akter, national coordinator, child protection at World Vision Bangladesh said: "Child protection issues are at the centre of the refugee crisis which include child marriage and child exploitation, and human trafficking.
"As different child trafficking groups are active in the region, children and adolescents, especially girls are vulnerable to trafficking."
World Vision has worked with a woman named Razia who fled Myanmar with her husband and children.
Her and her four-year-old daughter, Fiza, have had their names changed for security reasons.
Razia said Fiza was almost taken by a stranger in the middle of the night.
She told World Vision: "There are no permanent walls on the sides of the tent.
"From one side it's completely open. The shelter walls are so thin anyone can rip it open.
"We were all asleep. I keep the little one in the middle and the older children sleep on the sides. A man entered our tent from the side of the tent and picked up my 4-year-old.
"Luckily her elder daughter, seeing a silhouette of a stranger, let out a loud scream and woke up the family."
The family then woke up and the intruder left the child and ran.
Razia added: "We left to keep our children safe from the violence but after the incident we feel more vulnerable. We keep the children at home most of the time."
World Vision has called for "urgent care and attention" to the issue.
According to the UN Refugee Agency, international donors have pledged $344 million to help deliver critical humanitarian assistance to refugees and host communities in Bangladesh.
Jared Berends, senior director of operations and resource mobilisation at World Vision Bangladesh said: "We need to see a commitment within this funding to address the specific issue of protecting children, keeping them safe and out of reach of those who would prey on them."