The execution of Nimr al-Nimr and the others, including Shiite activists and Sunnis accused of involvement in deadly Al-Qaeda attacks, was announced by the Saudi interior ministry.
It prompted calls for demonstrations, with the brother of the 56-year-old cleric warning it could stir more trouble in oil-rich Eastern Province where Shiites complain of marginalisation.
"This action will spark anger of (Shiite) youths" in Saudi Arabia, said Mohammed al-Nimr.
The interior ministry said the 47 men had been convicted of adopting the radical "takfiri" ideology, joining "terrorist organisations" and implementing various "criminal plots".
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One of those executed was Fares al-Shuwail, described by Saudi media as Al-Qaeda's top religious leader in the kingdom. He was arrested in 2004.
Notably absent from the list, however, was Nimr's nephew, Ali al-Nimr, whose arrest at the age of 17 and alleged torture during detention sparked condemnation from rights watchdogs and the United States.
All those executed were Saudis, except for an Egyptian and a Chadian.
Some were beheaded with a sword while others were executed by firing squad, said interior ministry spokesman Mansur al-Turki.
Today's executions drew condemnation from Shiite-majority Iran and Iraq, and calls for anti-Saudi protests.
"The Saudi government supports terrorist movements and extremists, but confronts domestic critics with oppression and execution," said Hossein Jaber Ansari, spokesman for Iran's foreign ministry.
"The Saudi government will pay a high price for following these policies," the official IRNA news agency quoted him as saying.
He said Nimr's execution "merely shows the extent of irresponsibility and impudence".
"We are completely confident with what we're doing and we believe in it and do not care how others view our procedures, whether on justice or implementation of sentences," he told a news conference.