An Express News screen grab of murder convict Ikramul Haq
The hanging brings to 19 the number of executions Pakistan has carried out since it lifted a six-year moratorium on the death penalty in terror cases following a school massacre last month.
Haq execution was cancelled but later reinstated after a court rejected a pardon from his victim's family, officials said.
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Haq had been sentenced to death by an anti-terror court in 2004 for killing a Shia three years earlier.
Police, prison officials and defence lawyer Ghulam Mustafa Mangan confirmed the execution.
The victim's family had pardoned him on January 8 just before his scheduled hanging, but a court later rejected the compromise.
"The victim's family had pardoned my client, but the court rejected it and while we were appealing against the decision, my client was hanged," Mangan told AFP.
Murder can be forgiven under Pakistani law in exchange for blood money, while rival militant groups may choose to pardon each others' convicted killers.
The United Nations, the European Union, Amnesty International and Human Rights Watch have called on Pakistan to re-impose its moratorium on the death penalty, which ran from 2008 until December 2014.
Rights campaigners say Pakistan overuses its anti-terror laws and courts to prosecute ordinary crimes.
There are also concerns that death row convicts from non-terror related cases could be executed.
Taliban gunmen stormed an army-run school in the northwestern city of Peshawar last month, killing 150 people, mostly children, in the country's deadliest ever militant attack.
In addition to ending its death penalty moratorium, Pakistan has since moved to set up military courts to try terror cases.
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