During the French Revolution, Basel temporarily allowed a number of Jews in, officially forming a community in 1805. By 1864 the Basel Jewish community had grown to 300 souls, however, between then and emancipation, they were under severe civil and religious restrictions. Contemporary Basel Jews date their community from this time. In 1868 the single-domed synagogue was built. After full civil rights were granted in 1874 the Jewish community experienced significant growth.

The First Zionist Congress was held in Basel in 1897. It was originally supposed to be held in Germany but was moved to Basel because of rabbinical protests in Germany. It was Herzl's wish to center the Zionist movement in Basel, with a special congress building there, but his wish was never realized. However, Basel was the host of nine more congresses: including the second, attended by Chaim Weizmann, the sixth - in which the Uganda plan was proposed, the tenth - the first conducted in Hebrew, and the twenty-second - the last held outside of Israel in 1946. At the Congress in 1929, held in Switzerland, the Jewish Agency was formed.

Many Jews from Alsace and Eastern Europe immigrated to Switzerland in the nineteenth and twentieth centuries. In 1903, a Jewish cemetery was opened in Basel. Between then and 1947, several other synagogues were built. In 1947, the Great Synagogue (originally built in 1868) was restored.