Adel Habara was hanged in a Cairo prison days after a court upheld his death sentence.
He was convicted of involvement in a shooting that killed 25 policemen, days after police killed hundreds of demonstrators in Cairo protesting against the army's overthrow and detention of Islamist president Mohamed Morsi.
His execution came days after the Islamic State group claimed responsibility for a deadly Cairo church bombing that sparked renewed calls for speedier punishment of Islamist militants.
IS is waging an insurgency in the Sinai that has killed hundreds of policemen and soldiers since Morsi's overthrow.
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Habara had become a symbol for them of a slow appeals process. He had been sentenced to death in an initial trial but was granted a retrial on appeal.
President Abdel Fattah al-Sisi, who toppled Morsi when army chief, had ordered changes to the law to speed up the judicial process after a car bomb killed the country's top prosecutor in 2015.
Habara is the eighth convicted militant whose execution has been announced since Morsi's overthrow.