"We are estimating that at least 17,000 pupils were killed in schools, that's the one number that we have some estimate on," UN Children's Fund executive director Ann Veneman told reporters in Islamabad.
According to Unicef estimates some 1.6 million to 2.2 million children have been affected by the earthquake, which has killed more than 55,000 people and made 3.3 million homeless.
Veneman said even those children who have survived were traumatised.
"The trauma that these children have experienced I think has been particularly even worse than other tragedies like the tsunami, because so many of these kids were in schools," she said.
"They were in school at that time when so many of school buildings came down. The ones that survived, many have injuries, many lost friends, they lost teachers, they lost important people in their lives."
The Unicef chief repeated warnings about a "second wave" of deaths if children are not provided with proper health care, clean drinking water and immunisation against disease.
"We are concerned about the possibility of a second wave of loss of life if children don't get the right interventions," she said. A Unicef statement quoting the government estimates said that 6,700 schools have been destroyed in North Western Frontier Province and another 1,300 in Azad Kashmir.
The agency was addressing psychological needs of teachers as well the requirements of nearly 20,000 children "who will have physical impairments after this tragedy due to injuries and amputations," it said.
"This figure may increase as more villages are reached," it said.