The statement did not elaborate on the intended topics of discussion. The two leaders will meet five days before Israel's April 9 election in which the right-wing Netanyahu faces a strong challenge from a centrist candidate.
On Monday, Netanyahu told reporters he and Putin spoke by telephone about Syria, whose Russian-backed president, Bashar Assad, has been gaining ground in an eight-year civil war.
Israel worries Assad's Iranian and Lebanese Hezbollah reinforcements could set up bases to attack it from Syria, and has carried out scores of air strikes against them.
Russian defense officials have on several occasions demanded that Israel ends its "arbitrary" airstrikes on targets in Syria, calling them "provocative."
Thursday's meeting could also help Netanyahu in the closely contested election, in which he has played up his statecraft and security credentials in the face of the politically untested challenger Benny Gantz, a former military chief.
In February the two leaders met - at the Kremlin in Moscow - for the first time since the incident in September when Syria accidentally downed a Russian plane during an Israeli aerial assault in the war-battered country, which sparked an international crisis. Following the meeting a senior Israeli official said both sides are willing to put the incident behind them.