The Sephardic Museum occupies the former Convent of the Knights of Calatrava, annexed to the Synagogue of El Tránsito, and displays historical, religious and customary aspects of the Jewish past in Spain, as well as those of the Sephardim, the descendants of the Jews who lived on the Iberian Peninsula until 1492.

In 1964, it was decided that the Synagogue of El Tránsito or the Synagogue of Samuel ha-Leví should be the headquarters of the Sephardic Museum, whose aim is to conserve the legacy of Spanish-Jewish and Sephardic culture so that it becomes an essential part of the Spanish Historical Heritage, a task it has carried out to this day. In accordance with the provisions of Royal Decree 1305/2009, of 31 July, which creates the Network of Museums of Spain, the Sephardic Museum is one of the National Museums owned and managed by the State, attached to the Ministry of Culture.

It is a Spanish National Museum attached to the Ministry of Education, Culture and Sport, and is managed exclusively by the Directorate General of Fine Arts and Cultural Heritage.

The first room shows the history, geography and culture of the Jewish people in the Ancient Near East, where, according to biblical writings, the traditions that survive in their daily lives originated. Archaeological artefacts dating from between 2000 BC and the 1st century AD are on display, as well as a wide variety of cultural objects related to what it is and what it means to be Jewish, their beliefs and customs. Highlights include a Torah (the holy book of Judaism, consisting of the Pentateuch) and other liturgical objects.