Sheikh Nimr al-Nimr was among 47 put to death after being convicted of terrorism offences, it said in a statement.
He was a vocal supporter of the mass anti-government protests that erupted in Eastern Province in 2011, where a Shia majority has long complained of marginalization.
Sheikh Nimr al-Nimr’s arrest the following year triggered days of unrest.
His death sentence was confirmed in October 2014.
Sheikh Nimr al-Nimr’s family said he was found guilty of seeking “foreign meddling” in the kingdom, “disobeying” its rulers and taking up arms against the security forces.
Shia-led Iran – the main regional rival of Sunni-ruled Saudi Arabia – said Riyadh will pay a “high price” for executing Sheikh Nimr al-Nimr.
Those also put to death include Sunnis convicted of involvement in al-Qaeda-linked terror attacks in 2003, reports said.
Of the 47 executed, one was a Chadian national while another was Egyptian. The rest are Saudis.
Protests broke out in early 2011 in the oil-rich Eastern Province in the wake of the Arab Spring.
Sheikh Nimr al-Nimr ‘s supporters say he supported only peaceful demonstrations and eschewed all violent opposition to the government.
He had been a persistent critic of Saudi Arabia’s Sunni royal family.
His brother, Mohammed al-Nimr, said he hoped any reaction to the execution would be peaceful.
A lawmaker in Iraq’s governing Shia coalition said the death aimed at “provoking sectarian fighting”, while Lebanon’s Shia council called it a “grave mistake”, Reuters reported.
Saudi authorities deny discriminating against Shia and blame Iran for stirring up discontent.
Saudi Arabia carried out more than 150 executions in 2015, the highest figure recorded by human rights groups for 20 years.
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