During his visit, which started on Thursday, the Israeli leader thanked the Lithuanian government for its efforts to preserve the Jewish heritage and fight anti-Semitism.
More than 90 percent of Lithuania's pre-war Jewish population of about over 200,000 was killed during the Nazi German occupation between 1941 and 1944.
Netanyahu also has Litvak roots as his grandmother was born in Šeduva, a town in Lithuania, and his grandfather was born in Krėva, in what is now Belarus.
Around 3,000 Jews now live in Lithuania.
"Jews from all regions of Lithuania will gather for the historic meeting at the Vilnius Choral Synagogue, which celebrates its 115th anniversary. It is important for the community to maintain a direct relationship between the state of Israel and the diaspora," she said.