The charity Save the Children says the majority of victims of rape and other sexual violence in many of the world's conflict zones are children.
Its report is based on data and testimonies from several countries including Colombia, Liberia and the Democratic Republic of Congo.
Save the Children says programmes to stop such violence and help children recover are chronically underfunded.
The issue will be discussed by foreign ministers of the G8 group this week.
The UK has said it will give priority to the issue of sexual violence in conflict during its presidency of the G8 this year.
Save the Children's report - Unspeakable Crimes Against Children  - says figures from a range of countries affected by conflict over the past decade show that children are often the majority of sexual abuse victims in war and its aftermath.
A study in Liberia - still recovering from civil war - found that 83% of victims of gender-related violence in 2011-12 were below 17 and almost all of them were raped.
In post-conflict Sierra Leone more than 70% of sexual violence cases seen by the International Rescue Committee were girls under 18, and more than a fifth of those were girls under the age of 11, the report says.
In Democratic Republic of Congo nearly two-thirds of sexual violence cases recorded by the UN in 2008 involved children, mostly adolescent girls.
Girls and boys are being kidnapped and abused by armed forces and groups, the charity says, and children as young as two are caught up in the violence.
It says many children will bear life-long psychological scars.
Save the Children's Chief Executive Justin Forsyth said: "It is shocking that in conflict zones around the world children are being raped and abused at such an appalling rate. Sexual violence is one of the hidden horrors of war and the damage it wreaks ruins lives.
"Even if they recover from the physical effects of their experiences, many victims carry the psychological scars of their ordeal for the rest of their lives, and are often cast out from society. Despite all this, there are huge gaps in funding for the work needed to protect children from these atrocious crimes and to respond to their needs."
The G8 foreign ministers - from the UK, Canada, France, Germany, Italy, Japan, Russia and the US - are meeting in London. They will hold a dinner on Wednesday and formal talks on Thursday.
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