Reyhaneh Jabbari, 26, was hanged in a Tehran prison on Saturday morning. She had been convicted of killing a man she said was trying to sexually abuse her.
Jabbari was arrested in 2007 for the murder of Morteza Abdolali Sarbandi, a former intelligence ministry worker.
Human rights group Amnesty International said her execution was “deeply disappointing in the extreme”.
Both the US State Department and British Foreign Office condemned the execution.
UK Foreign Minister Tobias Ellwood MP called on Iran to abolish the use of the death penalty.
“The UN noted that her conviction was allegedly based on confessions made while under threat. I urge Iran to put a moratorium on all executions,” he said in a statement.
A campaign calling for a halt to the execution was launched on Facebook and Twitter last month and appeared to have brought a temporary stay in execution.
However, government news agency Tasnim said on Saturday that Jabbari had been executed after her relatives failed to gain consent from the victim’s family for a reprieve.
It said her claims of self-defence had not been proved in court.
A Facebook page set up to campaign for a stay now says simply: “Rest in peace”.
After her arrest, Jabbari had been placed in solitary confinement for two months, where she reportedly did not have access to a lawyer or her family.
She was sentenced to death by a criminal court in Tehran in 2009.
Amnesty International said she was convicted after a deeply flawed investigation.
Hassiba Hadj Sahraoui, Amnesty’s Deputy Director for the Middle East and North Africa Programme said: “This is another bloody stain on Iran’s human rights record.”
“Tragically, this case is far from uncommon. Once again Iran has insisted on applying the death penalty despite serious concerns over the fairness of the trial.”
Amnesty said that although Jabbari admitted to stabbing Abdolali Sarbandi once in the back, she alleged that there was someone else in the house who actually killed him.
Jalal Sarbandi, the victim’s eldest son, said Jabbari had refused to identify the man.
He told Iranian media in April: “Only when her true intentions are exposed and she tells the truth about her accomplice and what really went down will we be prepared to grant mercy,”
The United Nations says Iran has executed about 250 people this year.