Hussein al-Saket, 22, was found guilty of abducting, raping and murdering a four-year-old girl, who he later buried, said Rajeh Ezzedine, a judge who attended the execution.
Ali Ayedh, the victim's uncle, said Saket "took part in the search for the girl before being unmasked" during the police investigation.
He said his public execution would act as a "deterrent for criminals".
Saket was placed face down on Tahrir square in Sanaa, which the Shiite Huthi rebels have controlled since 2014.
On July 31, another man was executed in the same square after being convicted of raping and murdering a three-year-old girl.
Both executions have been framed as an example of the Shiite rebels' efforts to combat crime in their areas.
The Iran-backed Huthis have been locked in war with the Saudi-backed government of President Abedrabbo Mansour Hadi for more than two years.
More than 8,300 people have been killed and millions displaced in the conflict, while some 2,000 have died of cholera since April.
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