The death of Adnan al-Ghoul was confirmed both by Hamas and the Israeli military, the report said.
Hamas spokesman Mushir al-Masri said he was killed as he rode in a vehicle in Gaza City. The group vowed to take revenge.
The Israeli military launched the Gaza operation last month to destroy Qassam rockets filled with explosives that have been used to attack various Israeli towns.
Dozens of Palestinians and five Israelis, including two soldiers, have been killed since the operation began.
The Israel Defense Forces said it had targeted al-Ghoul because he was a leading figure behind the development and production of Qassam rockets.
In other incidents, an Israeli soldier was killed Thursday in an explosion on the border between Rafah in the Gaza Strip and Israel.
Israel Radio said the soldier was wounded seriously when an explosive device targeted an army patrol in the area. He died later in hospital.
Al-Qassam Brigades, the military wing of Hamas, claimed responsibility for the blast.