The strike in the northern Gaza Strip came amid an escalation in violence between Palestinian fighters in Gaza and Israel.
The Israeli military said it targeted two Islamic Jihad militants from the group's rocket launching unit who were posing an immediate threat. The Gaza health ministry reported one dead and several wounded.
Earlier Tuesday, Israel killed an Islamic Jihad commander and wounded seven others in a strike in the Gaza Strip, sparking retaliatory rocket fire into Israel from the Palestinian enclave.
Israel accused the commander, Baha Abu Al-Ata, 42, of being behind recent rocket fire into Israel and a range of other attacks.
It alleged he was planning further attacks and called him a "ticking bomb."
The strike and rocket fire, which caused damage and a number of injuries in Israel, raised the possibility of a severe flare-up between the two sides.
The Israeli military said around 50 rockets had been fired and its air defences had intercepted about 20 of them.