The executions, by firing squad, took place just 24 hours after the two men, 25-year-old Said al-Barawi and 26-year-old Faisal Abu-Talaikh were convicted by a court in Gaza.
They pleaded guilty to taking the child to a deserted area near the Rafah refugee camp last week where they raped her and then hit her with a blunt object, before burying her.
The body was found on Saturday.
International outcry
The two men were executed at a security headquarters in Gaza City, according to Palestinian security officials. Hospital officials confirmed their deaths soon after.
Palestinian courts have handed down several death sentences since the Palestinian Authority came into existence in 1994, but few of the verdicts have been carried out.
In January 2001, the Authority publicly executed two Palestinians shortly after their conviction for collaborating with Israel.
The sentence provoked criticism from Palestinian and international human rights organisations who urged the Authority to end use of the death penalty.
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