Unicef says almost 26,000 children - most of them unaccompanied - crossed the Mediterranean last year.
In its new report, Unicef says many children suffer from violence and sexual abuse at the hands of smugglers and traffickers.
But they rarely report their abuse, for fear of arrest and deportation.
The agency also says there is a lack of food, water and medical care in Libya's detention centres.
The plight of children, many of them unaccompanied by parents, has become a tragically familiar part of the wider story of mass migration over the past two years.
But while much has been said about the extreme dangers faced at sea, the privations experienced on land, especially in Libya, are less familiar.
Unicef's latest report, A Deadly Journey for Children, documents - in sometimes horrific detail - stories of slavery, violence and sexual abuse experienced by huge numbers of vulnerable children making their perilous way to Italy.
"What really shocked Unicef staff and me... is what happens to them [children] on this route," says Justin Forsyth, the organisation's deputy executive director. "Many of these children have been brutalised, raped, killed on this route."
Girls such as nine-year-old Kamis, who set off with her mother from their home in Nigeria. After a desert crossing in which a man died, followed by a dramatic rescue at sea, they found themselves held at a detention centre in the Libyan town of Sabratha.
"They used to beat us every day," Kamis told the researchers. "There was no water there either. That place was very sad. There's nothing there."
Much of the violence is gratuitous, and much of it is sexual.
"Nearly half the women and children interviewed had experienced sexual abuse during migration," the report says. "Often multiple times and in multiple locations."
Borders, it seems, are particularly dangerous.
"Sexual violence was widespread and systemic at crossings and checkpoints," says the report.
Many of the assailants are in uniform. This is said to be just one reason why those who suffer abuse are reluctant to report their experiences.
And Libya, as the funnel through which so many journeys pass, has earned itself a shocking reputation as the epicentre of abuse.
"Approximately one third [of those interviewed] indicated they had been abused in Libya," the report says. "A large majority of these children did not answer when asked who had abused them."
So commonplace are stories of rape and sexual enslavement that some women embarking on the journey take precautions, such as getting contraceptive injections and carrying emergency protection with them.
The report maps 34 known detention centres in Libya, three of them deep in the country's desert interior.
Most are run by the government's Department for Combating Illegal Migration. But Unicef says that armed groups also hold migrants in an unknown number of unofficial camps.
"The detention centres run by militias, we're much more worried about," says Mr Forsyth. "That's where a lot of abuse is happening and we have very, very limited access."
In 2016, more than 180,000 migrants crossed from Libya to Italy. According to the UN, almost 26,000 of these were children, most of them unaccompanied. The number of unaccompanied children appears to be soaring.
"It's a combination of factors," says Mr Forsyth. "The situation in places like Eritrea and northern Nigeria is very bad. Also in the Gambia recently."
'I wanted to cross the sea'
Politics aside, poverty and the promise of a better life remain key drivers.
"I wanted to cross the sea," 14-year-old Issaa told researchers. "Look for work, work hard to earn a bit of money to help my five brothers at home."
But two and a half years after leaving home in Niger, Issaa was found living alone in a Libyan detention centre.
"My father collected money for my journey, he wished me luck and then let me go."
The migrants are, of course, heavily dependent on smugglers to get them through the desert and across the sea.
A recent case when dozens bodies were found washed up on the shore near the western city Zawiya shows that this remains extremely hazardous.
But smuggling is all-too often associated with human trafficking. Victims accept migration packages from criminal gangs, only to find themselves forced into prostitution to repay their debts.
"Libya is a major transit hub for women being trafficked to Europe for sex," the report says.
Libya's continuing political turmoil makes it extraordinarily difficult to tackle a phenomenon, which the report says has spiralled out of control.
But Unicef is urging Libya, its neighbours and regional organisations to do more to protect children.
A regional initiative, it says, would include improved birth registration, the prevention of trafficking, safe and legal pathways for children fleeing armed conflict and, where appropriate, family reunification.
"Whether they're migrants or refugees, let's treat them like children," says Mr Forsyth. "It's a reflection of our humanity, our values, how we respond to this crisis."