Shafqat Hussain, whose case sparked international outcry on the grounds that he was a juvenile at the time of crime in 2004, was executed in Karachi Central Prison in the wee hours.
Shortly after the news of the hanging spread human and civil right activists took out protest marches in Karachi, Islamabad and some other parts of the country protesting the execution.
Gul Zaman, brother of Hussain, told PTI that his family had done their best to help his brother but all efforts failed.
Hussain, a resident of Pakistan-occupied Kashmir, was arrested and convicted in 2004 for the kidnapping and killing of a seven-year-old boy in Karachi. All of hia appeals were turned down.
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Initially he was scheduled to be hanged on January 14 but the execution was to be postponed as a controversy cropped up about his age.
Various local and international human rights groups contended that he was convicted at the age of 14 and was deprived of the juvenile laws.
United Nations rights experts have said his trial "fell short of international standards" and asked Pakistan to investigate claims he confessed under torture, as well as his age.
Those opposing his hanging said the issue of age was overlooked.
Interior Minister Nisar Ali Khan ordered an inquiry in March to establish the veracity of the lawyers' contention that Hussain was a minor at the time of sentencing.
After a probe, it was found that Hussain was 23 at the time of crime.
But the legal wrangling went on as the Hussian's lawyer first challenged the case in Islamabad High Court which rejected their pleas.
Later, the case was taken to the Supreme Court which also rejected arguments about his age. The hanging was postponed four times.
Pakistan has hanged around 180 convicts since restarting executions.