The 8 October South Asian earthquake killed at least 17,000 children when their schools collapsed, the UN children's fund, Unicef, says.
Unicef fears there could be "second wave" of child deaths
It said those that survived were either injured or suffered the trauma of losing friends and teachers.
It also warned of a second wave of deaths if children did not get health care, clean water and immunisations.
Pakistan says the quake killed more than 55,000 people, injured another 78,000 and left three million homeless.
Another 1,400 died in Indian-administered Kashmir.
Unicef says Pakistan government estimates show 6,700 schools were destroyed in North-West Frontier Province and 1,300 in Pakistan-administered Kashmir as children attended morning classes.
Ann Veneman, Unicef executive director, said the trauma suffered by the children who survived could well be worse than those who escaped last December's Asian tsunami.
"The ones that survived, many have injuries. The ones that survived, also many lost friends. They lost teachers, they lost important people in their lives."
Unicef estimates nearly 20,000 children "will have physical impairments after this tragedy due to injuries and amputations".
Ms Veneman also said there was a continuing threat to the wellbeing of the survivors.
"We are concerned about the possibility of a second wave of loss of life if children don't get the right interventions."
Ms Veneman repeated appeals for more aid from the international community, saying it had only provided a fraction of what was needed.
The UN has asked for $550m but has so far received pledges of only $327m.
The UN is leading a massive relief effort to try to get aid to the millions of people affected before the harsh Himalayan winter sets in.
On Monday, Pakistani President Pervez Musharraf vowed to deliver 500,000 tents by the end of November.
Relief groups say about 800,000 people still lack shelter.
President Musharraf defended the relief effort.
"I am fully confident that we will meet the challenge and I will prove the cynics wrong," he said.
Pakistan also said it had set up two relief camps on the Line of Control that separates Indian and Pakistani-controlled Kashmir. India has set up three on its side.
The move came after the nations agreed on Saturday on a landmark opening of the Line of Control to help quake victims.
Relief items can be sent in both directions and families will be able to cross at five points from 7 November - but only on foot. No vehicle crossings will be allowed.
People wanting to cross will need a permit from government officials on either side.