The government ended the six-year ban on capital punishment for terror-related cases following a brutal terror attack on a school in Peshawar on Tuesday that killed 149 people, mostly children.
"Yes, two militants Aqil alias Doctor Usman and Arshad Mehmood have been hanged in Faisalabad jail," Shuja Khanzada, Home Minister of central Punjab province, where the executions took place, told AFP.
A senior official from the prison department also confirmed the executions.
Aqil, who uses the name Doctor Usman, was convicted for an attack on the army headquarters in Rawalpindi in 2009 and was arrested after being injured.
Arshad Mehmood was convicted for his involvement in a 2003 assassination attempt on former president General Pervez Musharraf.
On Thursday, Pakistan's military chief signed death warrants for six terrorists on death row after the government ended the death penalty moratorium on Wednesday.
Just hours later, the government warned prison officials of a possible jailbreak in the restive northwest province of Khyber-Pakhtunkhwa amid fears that terrorist groups could try to spring high-ranking comrades from jails to avoid the noose.
The United Nations called for Pakistan to reconsider executing terror suspects, saying that "the death penalty has no measurable deterrent effect on levels of insurgent and terrorist violence" and "may even be counter-productive".
"We urge the Government not to succumb to wide-spread calls for revenge," said UN Human Rights Office spokesperson Rupert Colville.
Pakistan imposed a de facto moratorium on civilian executions in 2008, though hanging remains on the statute book and judges continue to pass the death sentence.
Only one person has been executed since then, a soldier convicted by a court martial and hanged in November 2012.
Rights campaign group Amnesty International estimates that Pakistan has more than 8,000 prisoners on death row, most of whom have exhausted the appeals process. The government says that more than 500 convicts are related to terror cases.