Hangings resumed after the country's bloodiest-ever militant attack, in which the Taliban gunned down 154 people -- mostly children -- at a school in the northwest.
Munir Hussain, who was convicted of a double murder in 2000, was hanged in the town of Vehari in Punjab province, said Syed Babar Ali Shah, superintendent of Vehari jail.
"He was convicted for murdering his nephew and niece with an axe over a property dispute in November 2000," said Shah, adding that Hussain was sentenced to death in 2001. A second prison official confirmed the execution.
Amnesty said Islamabad was gaining a reputation as one of the world's leading executioners.
Read: Executions: 12 convicted murderers sent to the gallows
A moratorium on the death penalty had been in force since 2008, but after the school attack it was lifted for those convicted of terrorism offences. In March it was extended to cover all capital offences.
The European Union, the United Nations and human rights campaigners have all urged Pakistan to reinstate the moratorium.
Critics say the country's criminal justice system is marred by police torture, poor legal representation for victims and unfair trials.
Amnesty estimates that Pakistan has more than 8,000 prisoners on death row, most of whom have exhausted the appeals process.
"In reaching this shameful milestone of 100 executions in just over four months, the Pakistani authorities are showing total disregard for human life," said David Griffiths, the group's deputy Asia Pacific director, in a statement.
"Our concerns are heightened by manifestly unfair trials in many cases that fall well below minimum standards set by international law. This conveyor belt of killing will do nothing to address the root causes of crime and terrorism, and must end immediately."
Read: 500 convicts to be hanged in coming weeks: Nisar
Campaigners have particularly highlighted the case of Shafqat Hussain, whose lawyers say he was a juvenile at the time of his murder trial. They say evidence obtained as a result of torture was used against him.
Hussain is due to be hanged on May 6 after the government ordered an investigation to try to determine his true age.
The probe, carried out by the Federal Investigation Agency, found Hussain was an adult at the time of his conviction, according to media reports, though its results have not been published officially.
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