Iranian Deputy Foreign Minister for Arab and African Affairs Hossein Amir Abdollahian conveyed Iran’s protest at the execution of the senior cleric to the Saudi envoy.
The execution of Sheikh Nimr has drawn widespread international condemnation.
Saudi Arabia executed 47 prisoners on Saturday, including Sheikh Nimr, the Arab country’s interior ministry said in a statement.
Among them were four Shiite Muslims accused of anti-government protests in recent years.
The executions took place in 12 cities in Saudi Arabia, four prisons using firing squads and the others beheading. The bodies were then hanged from gibbets in the most severe form of punishment available in the kingdom's law.
Sheikh Nimr was detained in July 2012 on charges of delivering anti-regime speeches and defending political prisoners.