Imran Ali, who was arrested after her body was found in a garbage dump, was executed in Lahore's Kot Lakhpat prison, police said.
Zainab's father and other relatives were present. Zainab's father, Amin Ansari told the BBC after the execution that he was "satisfied".
"I have seen his awe-inspiring end with my own eyes. They dropped him on the gallows, and let his body hang for half an hour," he told reporters.
The case, the most heinous in a string of similar child murders in the city of Kasur, had sparked outrage and protests in the country.
Zainab disappeared on January 4 and her body was found five days later in a rubbish dump. She would have been 7 years and 2 months old if she was alive, said Ansari, who expressed regret that authorities did not televise the hanging.
Ansari's earlier appeal for Ali to face a public hanging was dismissed by the Lahore High court.
Police said there had been several similar child murders in the past two years in Kasur but her killing proved to be a tipping point.
It triggered widespread outrage, including protests complaining of police incompetence. Two people were killed in the ensuing clashes.
Zainab's family had said the police did not take action during the five days from when she was reported missing until her body was found.
Relatives, not police, had recovered CCTV footage of her last movements.
It showed a girl being led away by a man. Widely circulated on social media with the hashtag #JusticeForZainab later went viral, with many Pakistanis calling for action.
On January 23, 24-year-old Imran Ali was arrested using a DNA match. He was sentenced to death in February for Zainab's rape and murder.
His appeals against the verdict failed and earlier in October President Arif Alvi rejected a plea for clemency.
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
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