World Vision says it is in urgent need of funds to meet the needs of growing numbers of Syrian refugees.
The warning comes as the United Nations estimates 10 million Syrians will be in need of aid by Christmas. Over a million refugees have crossed the border into neighbouring Lebanon.
World Vision says violations against children are "rampant" and that the influx of refugees into Lebanon has gone beyond the country's ability to cope.
Justin Byworth, Chief Executive of World Vision UK said the new figures from the UN confirmed that the crisis was "spiralling out of control".
"Syrian children are dying, hungry and homeless. We are desperately trying to help those refugees who need it the most but as the numbers continue to grow, we urgently need more funds to scale up our work," he said.
"A quarter of the Lebanese population are now estimated to be Syrian refugees, over one million people in a country of just 4 million. This has gone way beyond Lebanon's ability to cope.
"We are seeing tensions rising in communities, schools and hospitals. The situation has reached boiling point. The world must sit up and take notice of this widening humanitarian tragedy."
An estimated 80,000 people have died as a result of the Syria conflict. World Vision warned that children were being caught up in the fighting.
It pointed to a recent report from the Independent International Commission of Inquiry which found that children were being used in combat and falling victim to unlawful killings, detentions and abductions.
Around three million Syrian refugees are children.
Philippe Guiton, World Vision Syria crisis response leader says: "The clock has been ticking for two years, now the alarm is sounding too loud to be ignored. It is time to wake up to the size of the need and the seriousness of abuses against children."
World Vision is calling on the international donor community to increase funding to NGOs and UN agencies engaged in child protection work, as well as countries hosting Syrian refugees.
The aid agency also said there needed to be an end to "blurring the lines between humanitarian aid, politics and military action".
"Humanitarian assistance should not be conflated with military aid of any form. Humanitarian aid is delivered on the basis of humanitarian principles of impartiality, neutrality, humanity and independence," the agency said.