The three Shiite men faced the firing squad, six days after a court upheld their death sentences over a bomb attack in March 2014, the prosecutor's office said in a statement carried by BNA state news agency.
Bahrain, which has been ruled by the Al-Khalifa dynasty for more than two centuries, has a majority Shiite population which has long complained of marginalisation.
It has been rocked by sporadic unrest since March 2011 when security forces brutally crushed an Arab Spring-inspired uprising demanding reforms and a constitutional monarchy.
Pictures shared online by activists also showed relatives of those executed weeping over their deaths.
Authorities in Bahrain do not permit international news agencies to cover events independently.
The executions came a day after demonstrations broke out across Shiite villages following rumours that the authorities were going to put them to death.
They are the first in six years in the Gulf kingdom, according to London-based human rights group, Reprieve, which had warned on Saturday against the move.
Reprieve said the executions went ahead "despite serious concerns that their convictions were based on evidence obtained under torture."
Sayed Ahmed Alwadaei, head of advocacy at the Bahrain Institute for Rights and Democracy, said: "This is a black day in Bahrain's history."
"It is the most heinous crime committed by the government of Bahrain and a shame upon its rulers," he said in a statement.
Scores of men and women had taken to the streets yesterday after the families of the three were summoned to meet them in prison, a measure that usually precedes the implementation of death sentences, witnesses said.
"No, no to execution," the protesters chanted.
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