Zohur Hussein Mohammed Sadeq had been found guilty of smuggling heroin into Saudi Arabia, the ministry said in a statement carried by the official SPA news agency.
The previous day the ministry reported that a Saudi had been executed after he was found guilty of murdering a compatriot.
The latest beheading brings to 31 the total number of executions in the ultra-conservative kingdom so far this year, according to an AFP tally based on official reports.
Under the AFP count, at least 76 people were beheaded in 2011, while rights group Amnesty International put the number of executions last year at 79.
The death penalty in Saudi Arabia applies to a wide range of offences including rape, apostasy, armed robbery and drug trafficking, as well as murder, as stipulated by Sharia law.
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