Mohammed Ghafour Hashim Khan was convicted of smuggling “a large amount” of heroin into the country, the ministry said in a statement published by the official Saudi Press Agency.
The sentence was carried out in Eastern Province.
Khan’s case brings to 83 the number of foreigners and Saudis executed in the kingdom this year, including 11 Pakistanis since October, according to an AFP tally.
In addition to amphetamines and other drugs, authorities seized almost 18 kilogrammes (40 pounds) of raw heroin during the calendar year that ended in October, the interior ministry has said.
The government is battling narcotics “because of their great harm to individuals and society”, the ministry says, but foreign rights groups are critical of the kingdom’s judicial system.
Families and rights campaigners complain that the trials are opaque and unfair, and accuse the Pakistani government of doing nothing to help its citizens, afraid of offending an important and hugely wealthy ally.
In recent years the Gulf has become an increasingly important market for illicit drugs, according to the United Nations Office on Drugs and Crime.
Almost half of Afghanistan’s heroin production comes through Pakistan on its way to Europe and Asia.
In August and September alone, nearly 400 people, including around 300 foreigners, were arrested for possessing or dealing heroin, according to the Saudi government.
Rape, murder, apostasy and armed robbery are also punishable by death under Saudi Arabia’s strict version of Islamic sharia law.
Saudi Arabia had the third-highest number of recorded executions in 2013, behind Iran and Iraq, said Amnesty International.
The rights watchdog did not have reliable data from China which implemented the most death penalty sentences.