Neither of the attacks caused casualties, the Israeli army and Palestinian sources confirmed.
The firing of projectiles towards southern Israel is rarely claimed but such assaults are often attributed to radical groups inside impoverished Gaza.
Israel often blames Hamas, which rules the Palestinian territory, and usually retaliates against its armed wing by attacking its bases.
Overnight Wednesday the Israeli army said ‘a projectile was fired towards the south of Israel’.
‘In response to this attack, the air force targeted two terrorist Hamas positions in the northern Gaza Strip,’ it said in a statement.
At least two bombs were dropped on a training base of the Ezzedine al-Qassam Brigades, Hamas's military wing, in the central Gaza Strip, witnesses said.
Another strike was aimed at land in the east of the city of Gaza, according to sources within the Gazan security services.
No casualties were reported as a result of the raids, medical sources said.
Israel and Hamas have fought three wars since 2008.
Since the last round in 2014, a fragile ceasefire along the largely closed border has been observed.
In early February, the Islamic State group claimed responsibility for firing rockets into southern Israel from the Sinai Peninsula near the border with Gaza, the first since 2015.