Authorities executed Hafiz Wifaq Rasoul Shah in the Muslim holy city of Madinah, an interior ministry statement carried by the official Saudi Press Agency said.
“Investigations led to his confession and he was tried and found guilty,” the statement said.
Karachi is a key transit point for heroin from Afghanistan.
According to the United Nations Office on Drugs and Crime, the Gulf has become an increasingly important market for illicit drugs in recent years.
The Saudi government says it “is committed to fighting drugs of all kinds due to the physical and social harm they cause.”
Drug trafficking, rape, murder, apostasy and armed robbery are all punishable by death under the Gulf kingdom’s strict version of Islamic Shariah law.
Amnesty International said in its annual report released Wednesday that death sentences are often imposed “after unfair trials.”
The London-based watchdog said some defendants claimed to have been tortured or “otherwise coerced or misled into making false confessions” before trial.
According to an AFP count, the kingdom executed 87 people last year, up from 78 in 2013.