UNICEF said on Monday that of the two children beheaded, one had also been mutilated. (Agencies)
It also said it could verify the deaths of at least 16 children and 60 injured since the outbreak of fighting in early December.
"We are witnessing unprecedented levels of violence against children," said the UNICEF representative in Central Africa, Souleymasne Diabate.
"More and more children are being recruited into armed groups, and they are also being directly targeted in atrocious revenge attacks. Targeted attacks against children are a violation of international humanitarian and human rights law and must stop immediately," Diabate said.
Three weeks of conflict between Christians and Muslims have left some 1,000 people dead and displaced hundreds of thousands of others.
French and African troops are struggling to contain the unrest, which has wracked the majority Christian country since a March coup by mostly Muslim Seleka rebels who installed Michel Djotodia as president.
Djotodia has officially disbanded Seleka, but has proved unable to control the fighters who swept him to power, as the country descends further into sectarian violence.
UNICEF said that children forced into fighting by both sides in the conflict should be immediately disarmed and be protected from any reprisals. It also called for centers to be established for the "reintegration" of children as well as protect those still at risk.
The claims by UNICEF came as figures released by Doctors without Borders revealed they had treated more than 1,000 people in the capital Bangui throughout December.
In a statement, it said that in the past few days it had treated people suffering injuries caused by machetes, those who had received several stab wounds and some with other brutal injuries.
"We have also seen the arrival of people who have been tortured or brutally beaten. We also saw one case where a person had been impaled," said the statement.
UNICEF said on Monday that of the two children beheaded, one had also been mutilated.