As many as 300,000 living in Lebanon and Jordan could be without schooling by the end of 2013, BBC quoted UNHCR as saying.
Many of those not at school go out to work from as young as seven years old.
More than half of 2.2 million Syrian refugees are children, the UN says, with many facing grave dangers even outside the war zone.
Those perils include threats to their physical and psychological well-being, according to the report's authors.
Launching the report, UN High Commissioner for Refugees Antonio Guterres said: "If we do not act quickly, a generation of innocents will become lasting casualties of an appalling war."
The study is the latest to attempt to illustrate the heavy toll of Syria's three-year-old conflict on children both inside and outside its borders.
It comes shortly after an estimate from a London-based think-tank put the number of children killed during Syria's civil war at more than 11,000.
The UNHCR carried out a series of interviews with Syrian children and families living in Jordan and Lebanon between July and October 2013.
Researchers interviewed 81 refugee children and held group discussions with 121 others in Jordan and Lebanon, and consulted UN and NGO staff working with those communities.
They found high levels of child recruitment, labor and loneliness among children living in displaced families.
More than 70,000 Syrian refugee families now live without fathers, the UNHCR estimates, with some 3,700 refugee children living unaccompanied or without both parents.
Of the 1.1 million young Syrian refugees, 385,007 now live in Lebanon, 294,304 in Turkey and 291,238 in Jordan, figures show, with sizeable numbers also in Iraq and Egypt.
Those figures are in danger of overwhelming the ability of host nations to cope, the report says.
In Lebanon, the authors note, some 80 percent of Syrian children are not in school, with the number of Syrian school-age children on course to exceed the numbers enrolled in Lebanese school by the end of 2013.
And there was also evidence of high numbers of children being born "stateless", with host countries failing to register the majority of babies born in refugee camps.
Some 77 percent of 781 refugee infants sampled in Lebanon had no official birth certificate, the report says. Just 68 birth certificates were issued to babies in Jordan's Zaatari refugee camp between January and mid-October 2013.
BA/BA