It is generally said to have been the only synagogue in the country during the years it operated, although since then Sha'ar Hashamayim has opened in Sulawesi.

The Surabaya Synagogue building was a former private residence purchased by the Israelitische Gemeente Soerabaia congregation in 1948.

[5] Many of these Iraqi Jews had emigrated from the Netherlands or directly from Iraq to work in Surabaya as government officials, soldiers, or businesspeople.

[7][10] World War II was very difficult on the Surabaya Jewish community as they were interned in concentration camps by the Japanese along with most other Europeans in the Indies.

[7] However, despite the opening of the new building, the Jewish community in Surabaya was already declining in numbers and this affected the use of the synagogue.

[5] In the decade after it opened, the majority of the Jewish community in Surabaya emigrated to Israel, Singapore, the Netherlands, Australia or the United States.

[15] A large group left for Israel during 1948–50, and after that there was a steady emigration for various reasons including hostilities against Jews as a result of the Suez Crisis, or the Indonesian claim over Western New Guinea, which led to measures against foreign nationals living in Indonesia.

[19] In its final years the synagogue building gained some official recognition but also became the target of political demonstrations against the state of Israel.

It continued to be the focus of anti-Israel demonstrations; in March 2010 a student group attempted to raise a Palestinian flag over the building, but were prevented from doing so by the police.