Jews settled in Lithuania in the 14th century, coming from Germany and Poland, and were treated well by the local pagan rulers. Most were farmers, artisans, and estate managers. During this period, intermarriage between the ruling families of Lithuania and Poland drew the two countries closer, bringing Lithuania under the influence of Catholicism and reversing the favorable treatment of Jews.

In 1495, the Grand Duke Alexander expelled all Jews from the country. The expulsion edict remained in force for eight years. After returning in 1503, Jews resumed their respected place in the economic life of the country. By the mid-16th century, the influence of the Church and the enmity of the lower nobility intensified, and laws restricting Jewish dress and occupations were passed. The political union of Lithuania and Poland in 1569 brought no marked change to the Jewish position. On the whole, the rulers of the country protected the Jews from excessive restrictions. The Jewish population enjoyed a measure of self-rule within their own communities.

From 1623 to 1764, Jewish religious, economic, and social life was regulated by the Council of Four Lands (See Kahal), within which the important Jewish communities of Lithuania were represented. During the years of the Cossack uprisings which began in 1648 and were led by Chmielnicki, thousands of Jews were slaughtered and many communities in Lithuania destroyed. A partial healing of the wounds inflicted by the Cossacks came in the following century. The Jewish community of Lithuania became a center of Jewish learning. Great influence on the spiritual life of Jews was exerted by Rabbi Elijah Gaon of Vilna. His pupils, especially Hayim of Volozhin, were the founders of famous Talmudical academies, or yeshivot, in the country. Lithuanian Jewry played an important role in the dispute between Hasidism and their opponents, Mitnagdim. The bulk of Lithuanian Jewry remained aloof from the Hasidic movement, and was primarily devoted to the study of the Talmud.

During the late 19th century, Lithuania became fertile ground for the growth of the Haskalah, or Enlightenment movement. Here, modern Hebrew literature flourished and produced some of the greatest Hebrew writers: Micah Joseph Levinsohn, Abraham Mapu, and J.L. Gordon. Later in the 19th century, the Zionist movement, as well as the Socialist Bund, found numerous followers among Lithuanian Jewry. During the same period, due to economic hardships and Tsarist persecutions, a large number of Lithuanian Jews emigrated to the United States, South Africa, and other countries, where they established flourishing Jewish communities.

After World War I, Lithuania became an independent republic. In 1919, the Lithuanian government appointed a Ministry of Jewish Affairs and granted Jews full cultural autonomy. Jews enjoyed these rights for five years before they were curtailed and economic restrictions instituted. However, Jews retained some of their cultural autonomy and developed a government-supported school system with Hebrew and Yiddish as the languages of instruction. Lithuania also remained a center of Talmudic study. Yeshivot continued to exist in Slobodka, Telz, Panevezsh, and a number of other cities.

At the outbreak of the World War II, nearly 170,000 Jews (about 7% of the general population), lived in Lithuania, 40,000 of them in Kovno, the capital of the country. In 1940, Lithuania was annexed by Soviet Russia, only to fall into the hands of Nazi Germany in the following year. In 1942, mass murders of Jews were carried out with the help of the local populace, until almost all Lithuanian Jews were wiped out, save only those few who had managed to flee to other countries.

After World War II, Lithuania was incorporated into the Soviet Union. In 1993, after Lithuania gained independence from the former Soviet Union, the number of Jews remaining in Vilna and Kovno was about 8,000. Although a few synagogues still function in the cities of Vilna and Kovno, Jewish culture and educational institutions are virtually nonexistent. In 1997, the Lithuanian postal service issued a commemorative stamp of the Gaon of Vilna, now recognized as a Lithuanian historical personality.