The sentence against Amin Allah Zar Gul was carried out in Riyadh after he was “found guilty of trying to smuggle heroin in his gut”, the official Saudi Press Agency said.
The five other Pakistanis beheaded since October 15 are among 65 people executed this year in the kingdom.
The interior ministry says the government is battling narcotics “because of their great harm to individuals and society”.
A United Nations independent expert called in September for an immediate moratorium on the death penalty in Saudi Arabia.
Christof Heyns, the UN special rapporteur on extrajudicial, summary or arbitrary executions, said trials “are by all accounts grossly unfair” and defendants are often not allowed a lawyer.
He said confessions were obtained under torture.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia’s strict version of Islamic sharia law