Putin was welcomed in the Ben Gurion Airport outside Tel Aviv in an official ceremony by Israeli Foreign Minister Israel Katz and other officials.
The president is expected to hold meetings with Israeli Prime Minister Benjamin Netanyahu and President Reuven Rivlin.
He also plans to meet Yaffa Issachar, mother of Naama Issachar, a 27-year-old Israeli woman jailed in Moscow over drug charges.
The meeting comes amidst reports on Russian authorities preparing for her early release after the case sparked a wide protest in Israel.
Issachar, a backpacker who was on her way home after a trip in India, was arrested during transit through a Moscow airport. Russian authorities said 9.6 grams of marijuana were found in her backpack, which she says was not belong to her.
In October, she was sentenced for 7.5 years in prison over "drug trafficking."
Putin is also scheduled to attend a dedication ceremony of a monument honoring the veterans and victims of the siege of Leningrad in Gan Sacher in Jerusalem together with Rivlin and Netanyahu.