The execution of 42-year-old Esmail Jafarzadeh was shown in an amateur video shared on the state broadcaster's website.
He was hanged at dawn in the square of the small northwestern town of Parsabad, in Ardebil province.
The execution was held in public "to restore citizens'
Sense of security and relieve their troubled minds," Ardebil's prosecutor Naser Atabati told reporters.
Seven-year-old Atena Aslani went missing on June 19 after walking away from her street vendor father, sparking huge concern on social media.
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President Hassan Rouhani described the case as "horrendous" and called for swift justice.
It took less than a week to convict Jafarzadeh after his trial began in late August. His death sentence was confirmed by the supreme court on September 11.
Parsabad's public prosecutor Abdollah Tabatabayi later announced that Jafarzadeh had also confessed to the murder two years ago of a woman whose body was never found.
Its Islamic penal code allows the families of murder victims to ask for "blood money" in lieu of execution.
Iran has also been horrified by the murder of an eight-month-old girl, who was in a car when it was stolen while her father opened the gates to their home in a Tehran suburb.
She was found dead in the car six days later, and two men have been charged with murder.