The men were convicted in a mass terrorism trial, a case that activists have decried and that UN human rights experts had expressed concerns over.
Bahrain executed on Saturday two men convicted in two separate cases, one involving the killing of a police officer and the other the killing of a mosque imam, the public prosecutor said in a statement.
Rights groups identified two of the men as Shia activists Ali al Arab and Ahmed al Malali, who were sentenced to death last year in a mass trial along with another 56 men convicted and given jail terms on "terrorism crimes."
Saying they were part of a terrorist cell trained to use heavy weapons and explosives, the court jailed 19 for life and 37 for terms of up to 15 years.
The prosecutor's statement, which did not identify any of the men, said two of them were convicted for crimes including using an assault rifle to kill a police officer in 2017, in attacks orchestrated by what it called Iran-based ringleaders.
Bahrain accuses mainly Shia Iran of stoking militancy in the kingdom, which Tehran denies.
The Bahrain Centre for Human Rights and the Britain-based Reprieve rights group condemned the deaths in separate statements alleging their confessions were obtained under "torture."
"Last night's executions demonstrate, once again, Bahrain's callous disregard for international standards of due process," said Reprieve deputy head Harriet McCulloch.
According to Reprieve, 23 convicts in the kingdom are on death row.
In an 11th hour appeal for clemency, HRW's acting Middle East director Lama Fakih warned that King Hamad was committing a "grave injustice by ratifying the death sentences of the two men despite the allegations of torture and other serious due process concerns."
On the eve of the executions, Amnesty International's Middle East research director Lynn Maalouf said: "If the Bahraini authorities go through with these executions it would be an utterly shameful show of contempt for human rights."
Amnesty said the two men had been subjected in custody to electric shocks and beatings, while Arab had also had his toenails ripped out.
Bahrain has repeatedly denied taking discriminatory measures against its Shia citizens.