Entitled "Danger every step of the way", the UNICEF report said nine out of every 10 children arriving in Italy were unaccompanied minors, noting that more than 7,000 of them had arrived in the first five months of the year.
"The reason we are seeing more (unaccompanied children) is not clear at this stage," UNICEF's Sarah Crowe told a press conference in Geneva.
Since January 1, 2,859 people have died while attempting to cross the Mediterranean, many of them children, according to the International Organization for Migration.
Unaccompanied and separated children are at particular risk of abuse and exploitation, notably by the smugglers they rely on to get to Europe, UNICEF said.
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"Just about every child who arrives on the Italian island of Lampedusa or in Sicily has a harrowing story to tell," the report said.
Both boys and girls are subjected to sexual violence and forced into prostitution. Some of the girls are pregnant by the time they arrive on European shores.
"We should never forget that children on the move are first and foremost children, who bear no responsibility for their plight, and have every right to a better life," said Marie-Pierre Poirier, UNICEF's special coordinator for Europe's migrant crisis.
And with the arrival of summer in Europe, the numbers of those risking the Mediterranean crossing from Africa and the Middle East are set to rise, it warned.
There are currently 235,000 refugees and migrants in Libya and some 956,000 in the Sahel countries, and "many - if not most - of them" are hoping to make their way to Europe, the UNICEF report said.