The ministry, in a statement carried by state news agency SPA, said Eid al-Umairi was found guilty of having dealt with "large quantities of amphetamines".
His beheading raised to 21 the number of executions so far this year in the conservative Muslim kingdom, according to an AFP count based on official reports.
Last year, the UN High Commissioner for Human Rights denounced a "sharp increase in the use of capital punishment" in Saudi Arabia.
In 2013, there were 78 executions.