Hamad bin Meshehen al-Rashidi was found guilty of kidnapping and raping a seven-year-old boy before throwing him into a well and killing him, the ministry said in a statement carried by SPA state news agency yesterday.
Rashidi was executed in Qassim province, north of Riyadh.
In the other case, Issa bin Mohammed al-Rashidi was condemned of kidnapping and raping a minor, and attempting to kidnap another. He was executed in the northern Hail province.
Saudi Arabia beheaded 78 people in 2013, according to an AFP count.
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Last year, the UN High Commission for Human Rights denounced a "sharp increase in the use of capital punishment" there since 2011.
According to figures from rights group Amnesty International, the number of executions rose from 27 in 2010, including five, to 82 in 2011, including 28 foreigners.
In 2012, the number of executions dipped to 79, among them 27 foreigners.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's strict version of Islamic sharia law.