World Vision has called for immediate action, as it attends a conference being held in Italy today by the European Parliament and UNICEF to discuss the situation.
The organisation says around a third of the one million refugees making the 'treacherous' journey to Europe are children, adding that approximately 500 youngsters have lost their lives making the journey by sea.
Their call came as three migrant children drowned in the Aegean Sea, after their boat capsized near Agathanisi in Greece.
World Vision's Director of Advocacy, Deirdre de Burca, said: "2015 will be remembered for the heart-breaking image of [Aylan] Kurdi's lifeless body on a Turkish beach as a catalyst.
"Countless more children have lost loved ones, left homes and communities.
"They continue to be deprived of a normal life and of the rights they should enjoy, such as an education, a home and warmth of a family and time for leisure and play.
"Many of them suffer post-traumatic stress disorder when arriving at their destination in Europe and do not receive adequate treatment".
World Vision reports temperatures at the Miratovac refugee camp in Serbia have dropped to -11 degrees celsius this week.
It's joining other agencies for a meeting in Palermo on the Italian island of Sicily today to recommend a number of 'concrete actions to help governments address the European refugee crisis'.
Deirdre de Burca added: "The aim of this event is to bring the issue of the protection needs of children in the context of the EU refugee crisis to the very top of the EU's agenda.
"It will identify critical challenges and risks for children arriving in the EU - both for children coming with and without their parents.
"It will also launch a "Palermo Call for Children" for the protection of the rights of refugees and migrant children in this current crisis.
"Finally, it will explore concrete actions for follow up as a part of upcoming legislative packages to be adopted as part of the EU Agenda on Migration".