Israel's air force hit the Gaza Strip's Hamas rulers early Wednesday after Palestinians fired at southern Israel on Monday, the army said.
Late Tuesday night the military said that an undefined "projectile" was fired from Gaza towards southern Israel.
A spokeswoman told AFP that it was "very probably" a rocket but that it was not clear where it fell.
Palestinians in the coastal territory have recently fired both rockets and mortar rounds into the Jewish state.
On Wednesday an army statement gave Israel's reply to the latest fire.
"In response to the projectile fired from the Gaza Strip at Israel earlier, the Israel Air Force targeted a Hamas military compound in the southern Gaza Strip," it said, without elaborating.
There were no reports of casualties on either side.
A wave of rocket fire follows US President Donald Trump's statement on Wednesday recognising Jerusalem as the capital of Israel.