Mohammed Yousuf Ezzeddine was executed in the northern city of Qurayat, near the borders with Jordan, the ministry said in a statement carried by SPA state news agency.
His beheading brings to 41 the number of people executed in Saudi Arabia since the start of 2013, according to an AFP tally.
In 2012, the kingdom executed 76 people, according to a count based on official figures.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's strict version of sharia, or Islamic law.