Ansar Iqbal was hanged at the District Jail of Sargodha city in eastern province of Punjab.
A police official said that his body has been handed over to relatives for burial.
Iqabal was arrested in 1994 and charged with murder. Police determined that he was in early 20s which the court accepted and tried him as an adult.
The UK-based Reprieve rights group disputed it and said that two documents presented during the trial showed him as 15-year-old at the time of arrest.
"He (the President) must not ignore the law and the evidence any longer," it said in a statement.
It is not the first controversial hanging of a minor in Pakistan. Last month, Shafqat Hussain was executed despite serious concerns about his age. Hussain's lawyers had said that he was only 14-year-old at the time of murder he allegedly committed.
Pakistan does not allow the execution of a juvenile, but prosecutors argued Hussain was an adult at the time of the murder.
Pakistan has executed about 240 convicts since starting execution in December after militants attacked a school in Peshawar and killed about 150 people, mostly children.
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