"The execution of Shafqat Hussein is regrettable and in flagrant contravention of Pakistan's national and international obligations," Chair of the UN Committee on the Rights of the Child, Benyam Dawit Mezmur said in a statement.
Lawyers for Hussain, convicted of killing a child in 2004, say he was 14 when found guilty and his confession was extracted by torture.
However, Pakistani officials say there is no proof he was a minor when convicted.
The Secretary-General's Special Representative on Violence against Children, Marta Santos Pais, said the execution is "deeply saddening and goes against Pakistan's commitments to children's rights."
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Pakistan was one of the main supporters of the World Summit for Children in 1990, and was amongst the first States to ratify the Convention on the Rights of the Child, she said.
They asked the Pakistani authorities to reinstate the moratorium on the death penalty, conduct rigorous investigations into reported cases of children on death row, and adults on death row for offences committed while below the age of 18, and ensure a prompt and impartial investigation into all alleged acts of torture.