A ministry statement said the man, identified as Samy Ben Moe'ed Louify, lured the young relative to an undisclosed location, raped her and then strangled her with her own clothes.
After his arrest the man confessed and was transferred to a local court, where he given the death sentence.
He was executed by beheading Wednesday, BikyaMasr.com reported.
Some 78 people were executed in 2011 in Saudi Arabia, one of the leading countries to employ the death penalty globally.
In addition to beheading, stoning is also practiced in Saudi Arabia, with both forms of execution often carried out in public, drawing international criticism for their inhumane nature.
Anti-capital punishment activists around the world have campaigned against the kingdom's execution practices.