Both of the men had been convicted of militancy - one was hanged in Karachi jail, the other in prison in Lahore.
Appeals for mercy had been turned down by President Mamnoon Hussain.
More than 150 people, mostly children, were killed in the 16 December Taliban attack. The new executions come despite calls by the UN not to resume them.
Mohammad Saeed Awan, a member of the banned sectarian group Lashkar-e Jhangvi, was hanged in Karachi jail. He had been found guilty of shooting dead a police officer and his son in 2001.
The second man hanged on Thursday was named as Zahid Hussain alias Zahidu. He was convicted in 2004 of killing a policeman in the city of Multan two years earlier.
Their executions come after seven men convicted of militancy were hanged on Tuesday.
Pakistan has the world's largest number of death row inmates, with more than 8,000 people awaiting execution, human rights groups say.
The Pakistani authorities have hanged two more convicts, bringing to 18 the number of executions since a moratorium ended after the Peshawar school attack.