The court ordered authorities to cut off Muhammed Basheer al-Ramaly's head with a sword, tie his body to a wooden cross and place his head on a pole to deter other would-be killers, The Times of London reported.
Al-Ramaly was found guilty last February of abducting and raping five boys 3 to 7 years of age. The 3-year-old was left in the desert to die.
Amnesty International said there were reports al-Ramaly may have been suffering from a psychological disorder.
One Saudi Web forum said police were surprised when he laughed as he confessed to the rapes and murder.
Saudi Arabia has come under fire from human rights groups in the past for its high number of executions.
Last year there were 102 beheadings, Amnesty International says.