The 11 were killed by firing squad, Hamas-run website Al Rai said and warned that the same punishment will be imposed soon on others.
The executions came a day after Israel killed three top Hamas commanders in an airstrike in southern Gaza.
Hours after the targeted strike on the Hamas commanders, Ismail Haniyeh, the former head of the Hamas regime in Gaza, said, "After a senior operative is killed, we immediately continue on our path without hesitating or stepping back".
Seven civilians also were killed in the bombing of the house in southern Gaza where the leaders were located.
The IDF said the military leaders were responsible for "major terror attacks against Israelis."
Meanwhile, two Palestinians were killed in an Israeli airstrike on Nusseirat refugee camp early this morning, emergency services said.
Two more were killed in an air raid near neighbouring Deir al-Balah.
Ashraf el-Qedra, spokesman for the Ministry of Health in Gaza, said 72 Palestinians have been killed since the two sides resumed hostilities on Tuesday after the collapse of a ceasefire and talks aimed at finding a lasting end to the fighting.
El-Qedra said 2,087 Palestinians have been killed since the conflict began in early July. The United Nations estimates that around 70 per cent of the dead were civilians.
The fighting has killed 67 people on the Israeli side, almost all of them soldiers.
The truce fell apart after Israel reported that militants had started firing rockets again.
Since the fighting flared up again this week, 360 rockets have been fired from Gaza toward Israel, according to the Israel Defence Forces.
They have caused some injuries but no deaths. Israel's Iron Dome missile defence system has intercepted 56 of the rockets, the IDF said.
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