"We express our deep dismay at the execution," Rupert Colville, a spokesman for the UN High Commissioner for Human Rights, told reporters in Geneva.
Rizana Nafeek was only 17 when she was charged with murdering her employer's baby a week after arriving in Saudi Arabia in 2005.
She was found guilty of smothering the infant to death after an argument with the child's mother, and despite concerns about her trial and numerous appeals from Sri Lanka and the international community she was beheaded on Wednesday.
"We are deeply troubled by reports of irregularities in her detention and trial, including that no lawyer was present to assist her in key stages of her interrogation and trial," Colville said.
He pointed out that Nafeek had been tried in a language she did not understand with only poor interpretation at her disposal, and that she had claimed she had been forced to sign a confession under duress.
She said the baby died in a choking accident while drinking from a bottle.
He also stressed her young age at the time of the offence.
Saudi Arabia is just one of three countries in the world that imposes the death penalty for crimes committed by minors.
Sri Lanka recalled its ambassador to Saudi Arabia Thursday to protest the execution, after President Mahinda Rajapakse deplored the beheading that was
carried out despite his latest clemency appeal over the weekend.
The UN's right body also lamented Friday "the sharp increase in the use of capital punishment in the kingdom of Saudi Arabia since 2011."
According to figures from Amnesty International, the number of executions in Saudi Arabia have jumped from 27 in 2010, of whom five were foreigners, to 82 in 2011, including 28 foreigners.
In 2012, the number of executions slipped slightly to 79 people, including 27 foreigners.