Butha Mushtaq was the third Pakistan executed on drug charges in Saudi Arabia since October 15.
He was found guilty of smuggling heroin concealed in capsules which he had swallowed, and executed in the capital Riyadh, the ministry said in a statement carried by the official SPA news agency.
His execution brings to 59 the number of people beheaded in Saudi Arabia this year.
Last year, 78 people of various nationalities were executed in the Gulf Arab state.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's strict version of Islamic sharia law.