In a statement, the army said Ahmed Abu-Deka, who was deputy commander of the Islamic Jihad’s rocket force, was targeted by Israeli warplanes.
"He was directly responsible for the barrages of rockets fired toward Israeli civilians in the last few days," it added.
Islamic Jihad confirmed his killing in a statement, saying that Abu-Deka, who was among the leaders of the al-Quds Brigades, the group’s armed wing, was martyred in a “cowardly” assassination carried out by Israel in Khan Younis in the southern Gaza Strip.
The Palestinian Health Ministry in a separate statement announced that three Palestinians had been killed and six injured in fresh Israeli airstrikes.
With the latest casualties, the death toll from Israeli airstrikes on the Gaza Strip has risen to 28, according to the ministry.
Another 86 Palestinians have been injured in the air attacks.
Israel has killed five senior figures of the Islamic Jihad group, including Abu-Deka, in its attacks on Gaza in the past three days.
Later, Israel's national emergency medical service, Magen David Adom, announced that one person was killed and five others were injured when a rocket fired from Gaza hit a residential building in the city of Rehovot in central Israel.
It was Israel's first casualty since it began an operation against Islamic Jihad three days ago.
The Israeli army said the airstrikes are part of Operation Shield and Arrow, an offensive launched after rockets were fired from Gaza following the death of a Palestinian inmate who was on a hunger strike in an Israeli prison.
Palestinian factions also fired a barrage of rockets at Israel on Wednesday.
According to Palestinian figures, at least 130 Palestinians have been killed by Israeli forces since the start of this year. At least 19 Israelis have also been killed in separate attacks during the same period.