Netanyahu's two-day trip is his third to Russia since September and also comes as the two nations mark 25 years since the reestablishment of diplomatic relations.
The Israeli premier's office said the two leaders would discuss "implementing the understandings reached during Netanyahu's visit to Moscow in April".
They will also discuss "regional issues, including those pertaining to the fight against global terror, the situation in Syria and its surroundings, and the prospectives for the diplomatic process between Israel and the Palestinians", a statement read.
Russian forces back Syrian President Bashar al-Assad's regime in the conflict.
Israel opposes Assad but has sought to avoid being dragged into the war. However, it fears that the chaos in the neighbouring country could help strengthen its arch-enemy Hezbollah.
Netanyahu admitted publicly for the first time in April that Israel had attacked dozens of convoys in Syria which were transporting weapons to the Lebanese Shiite militia, which fights alongside Assad's forces.
In September, Netanyahu and Putin agreed to set up a "hotline" to avoid accidental clashes.
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