Shafqat Hussain, whose case sparked international outcry, was executed in Karachi Central Prison in the wee hours.
He was arrested and convicted in 2004 for the kidnapping and killing of a seven-year-old boy in Karachi. His all appeals were turned down.
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.
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Under Pakistan Juvenile Justice System, no one can be hanged for a crime committed before the age of 18.
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.
Later, the case was taken to the Supreme Court which also rejected arguments about his age. The hanging was postponed four times.
Pakistan lifted the ban on executions in December 2014 following a Taliban attack on a school in Peshawar that killed more than 150 people.
Pakistan has hanged around 180 convicts since restarting executions.