Lonay Khan was hanged this morning in New Central Jail Bahawalpur in Punjab province. He was awarded death sentence in 2001 for killing his brother-in-law.
His appeals were rejected and President had also turned down the mercy petition. Khan's last meeting with relatives was also organised a day before his hanging.
Security was beefed up in and around the prison during the hanging.
Pakistan resumed executions on December 17, 2014 a day after a Taliban attack on an army school in Peshawar that killed more than 150 people, mostly children.
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Initially executions were limited to terrorism offences but on March 10 the government decided to implement death penalty in all cases following the Peshawar school massacre in December.
The moratorium on executions had been in place since a democratic government took power from a military ruler in 2008.
Supporters of the execution argue that it is the only option to deal with the scourge of militancy but human rights group are highly critical of it.
Rights groups say many convictions are highly unreliable in Pakistan where criminal justice system barely functions and torture has often been used to extract confessions.