The Lithuanian and Georgian foreign ministers will also take part in a meeting of a bilateral European and Euro-Atlantic integration commission.
Issues to be discussed during the meeting include bilateral cooperation and the situation in Georgia in the run-up to Sunday's presidential election, the Lithuanian Foreign Ministry said.
Georgia seeks to become a member of the EU and of NATO, but its chances of joining these organizations in the coming years look slim.
Russia recognized the breakaway regions of South Ossetia and Abkhazia as independent states after a brief war with Georgia in 2008.
Thousands of Russian troops are stationed on a permanent basis in military bases in South Ossetia and Abkhazia, which are considered by the international community as occupied territories of Georgia.
As part of his visit to Vilnius, Zalkaliani is also to visit the House of Signatories and pay tribute to Lithuania's freedom fighters at the capital's Antakalnis Cemetery.