The history of the Jews in Indonesia began with the arrival of early European explorers and settlers, the first recorded Jews arrived in the 17th century. Most Indonesian Jews arrived from Southern Europe, the United Kingdom, the Netherlands, Belgium, Germany, France, the Middle East, North Africa, India, China, and Latin America. Jews in Indonesia presently form a very small Jewish community of about 500–1,000, from a nadir of about 20 in 1997. Judaism is not recognized as one of the country's six major religions, however its practices are allowed under Perpres 1965 No. 1 and article 29 paragraph 2 of the Constitution of Indonesia. Therefore, members of the local Jewish community have to choose to register as "Belief in One Almighty God" (Indonesian: Kepercayaan Terhadap Tuhan Yang Maha Esa) or another recognized religions on their official identity cards.

Presently, most Indonesian Jews live in Manado on the island of Sulawesi.

Through the writings of the traveler Abû Zayd Hasan al-Sîrafî about the Guangzhou Massacre in the An Shi Rebellion in the 7th century, it indicates that there was already a Jewish community in China, at least in Guangzhou, a port connecting China and India, trading ships for that port are thought to have passed through the islands of modern-day Indonesia. With the local climate of monsoon winds, ships had to anchor for months at various ports between the two locations, such as in the Malay Peninsula and the waters of Sumatra. A more definite picture comes from the Persian writer Buzurg ibn Shahriyar in his Aja'ib Al-Hind Barrihi wa Bahrihi wa Jaza'irihi ("Wonderful things about the land, seas, and islands of India") written in the 10th century. He wrote an Omanite Jew named Ish'âq bin al-Yahûdî who traveled to China and had stopped in Sarîra (Srivijaya). Other evidence can be seen based on the 13th Century notes of Avraham ben ha-Rambam, a Jewish leader from Cairo who issued a t’shuva for a wife who was in a position of bound, because her husband who was a trader from Aden to bilâd al-Hind (the Indies) left her and died on the way back. A thing to note is that he was a camphor trader from Fans'ûr, in Sumatra (now Barus). This indicates that there were Jews involved in trade within the Indonesian region in the past.

In the 1850s, Jewish traveler Jacob Saphir was the first to write about the Jewish community in the Dutch East Indies after visiting Batavia, Dutch East Indies. He had spoken with a local Jew who told him of about 20 Jewish families in the city and several more in Surabaya and Semarang. Most of the Jews living in the Dutch East Indies in the 19th century were Dutch Jews who worked as merchants or were affiliated with the colonial regime. Other members of the Jewish community were immigrants from Iraq or Aden which were mostly concentrated in Surabaya and Semarang.

According to the notes of Israel Cohen. Around 2,000 Jews resides in the colony prior to the second world war, several Jewish civil organizations were founded around this time, the most notable being Association for Jewish Interests in the Dutch East Indies. The World Zionist Organization also had several offices in the colony, such as in Batavia, Bandung, Malang, Medan, Padang, Semarang, dan Yogyakarta. Both organizations are known to raise funds for Zionist movements.

In 1930, a census by the colonial government recorded 1,095 Jews. By the late 1930s, the number had increased to 2,500 in Java, Sumatra, and other areas. But during the events of World War II, the number of Jews in the Dutch East Indies was estimated at 2,000. In general, Indonesian Jews (especially those of Dutch and European descent) suffered greatly under the Japanese Occupation of Indonesia, being exiled and forced to work in detention camps and having their properties confiscated by the Japanese forces.

During the Battle of Surabaya, at least one Jew was recorded fighting alongside the Nationalist forces. Charles Mussry who was of Iraqi Jewish descent fought alongside the people's militias to defend Indonesia's sovereignty. After the war, the Jews who were released faced many problems and changes in the political situation in Indonesia. In the 1950s, the nationalization of several foreign companies by Sukarno, in addition to the foreign political situation such as the Israeli-Palestinian Conflict, caused a lot of Jewish emigration from Indonesia. Only a small number of these Jews returned to the Netherlands, with the majority of the Jews opting to migrate towards Australia, United States and Israel instead. The Majority of the Iraqi Jews who also had Indonesian ancestry remained in Surabaya for a while, although eventually most of them migrated to Israel in 1958. The Jewish community in Israel who came from the Dutch East Indies and Indonesia, founded several association organizations, the most notable being Tempo Dulu by Shoshanna Lehrer.

At some point, during the Old Order period, Judaism was recognized as one of Indonesia's religion under the name Hebrani (lit. 'Hebrew'), although during the New Order, Jewish descendants were asked to assimilate with the local population and were categorized in the census with Christianity. Since the fall of the New Order and the beginning of the Reformation era, some Jewish descendants have begun to identify themselves and practice Judaism again, Most notably the Jewish community in North Sulawesi.