Israel bombed positions of Al-Quds Brigades, the military wing of the Palestinian group Islamic Jihad, early Friday in the cities of Khan Younis and Rafah in the southern Gaza Strip.
No casualties have been reported so far.
The Israeli army announced the operation on its Twitter account.
The army had claimed that two rockets had been launched from Gaza a few hours ago.
The situation escalated in Gaza early Tuesday after an Israeli airstrike killed Bahaa Abu al-Atta, a senior military commander of Islamic Jihad, and his wife Asmaa.
Two days of fighting between Israel and Islamic Jihad have left 34 Palestinians dead, including eight children and three women. More than 111 have been injured, including 46 children and 20 women.
A truce was reached in Gaza that went into effect on Thursday at 5 a.m. local time, but a lasting ceasefire appeared tenuous due to differences over its terms.