Several different religions are practised in Indonesia, which is officially a secular state without an established state religion. The first principle of Indonesia's philosophical foundation, Pancasila, requires its citizens to state the belief in "the one and almighty God". Although, as explained by the Constitutional Court, this first sila of Pancasila is an explicit recognition of divine substances (i.e. divine providence) and meant as a principle on how to live together in a religiously diverse society. Blasphemy is a punishable offence (since 1965, see § History) and the Indonesian government has a discriminatory attitude towards its numerous tribal religions, atheist and agnostic citizens. In addition, the Aceh province officially applies Sharia and implements different practices towards religious and sexual minorities.

Several different religions are practised in the country, and their collective influence on the country's political, economic and cultural life is significant. Despite constitutionally guaranteeing freedom of religion, in 1965 the government recognized only six religions: Islam, Christianity (Catholicism, under the label of "Katolik", and Protestantism, under the label of "Kristen" are recognised separately), Hinduism, Buddhism and Confucianism. In that same year, the government specified that it will not ban other religions, specifically mentioning Judaism, Zoroastrianism, Shinto, and Taoism as examples. According to a 2017 decision of the Constitutional Court of Indonesia, "the branches/flows of beliefs" (Indonesian: aliran kepercayaan)—ethnic religions with new religious movements—must be recognised and included in an Indonesian identity card (KTP). Based on data collected by the Indonesian Conference on Religion and Peace (ICRP), there are about 245 unofficial religions in Indonesia.

From 1975 to 2017, Indonesian law mandated that its citizens possess an identity card indicating their religious affiliation, which could be chosen from a selection of those six recognised religions. However, since 2017, citizens who do not identify with those religions have the option to leave that section blank on their identity card. Although there is no apostasy law preventing Indonesians from converting to any religion, Indonesia does not recognise agnosticism or atheism, and blasphemy is considered illegal. According to Ministry of Home Affairs data in 2024, 87.09% of Indonesians identified themselves as Muslim (with Sunnis about 99%, Shias about 1%), 10.45% Christians (7.38% Protestants, 3.07% Roman Catholic), 1.67% Hindu, 0.71% Buddhists, 0.03% Confucians, 0.04% Folk and others.

Until the beginning of CE, the peoples of Indonesia followed the local tribal Austronesian and Papuan ethnic religions and traditions.

Historically, immigration from the Indian subcontinent, mainland China, Portugal, the Arab world, and the Netherlands has been a significant contributor to the diversity of religion and culture within the archipelago. However, these aspects have changed due to some modifications made to suit the Indonesian culture.

Before the arrival of the Abrahamic religions of Islam, Christianity and Judaism, the prevalent religions in the region were the Indian religions of Hinduism and Buddhism. They were brought to the archipelago around the second and fourth centuries, respectively, when Indian traders arrived on the islands of Sumatra, Java and Sulawesi, and brought their religion. The Shaivite sect of Hinduism started to develop in Java in the fifth century CE. Hinduism had a decisive influence on the ideology of the one-man rule of the Raja, and was the dominant religion in Indonesia before the arrival of Islam. The traders also established Buddhism which developed further in the following century and several Hindu and Buddhist-influenced kingdoms were established, such as Kutai, Srivijaya, Majapahit, and Shailendra. The world's largest Buddhist monument, Borobudur, was built by Shailendra and around the same time, the Hindu monument Prambanan was also built. The peak of Hindu-Javanese civilisation was the Majapahit empire in the fourteenth century, and is described as a 'Golden Age' in Indonesian history.

Islam was introduced to the archipelago in the thirteenth century. Coming from Gujarat, India (some scholars also propose the Arabian and Persian theories), Islam spread through the west coast of Sumatra and then developed to the east in Java. This period also saw Islam-influenced kingdoms established, namely Demak, Pajang, Mataram and Banten. By the end of the fifteenth century, 20 Islam-based kingdoms had been established, reflecting the domination of Islam in Indonesia.

The Portuguese introduced Christianity in the 16th century, notably to the island of Flores and to what was to become East Timor. Protestantism was first introduced by the Dutch in the 16th century with Calvinist and Lutheran influences. For the Dutch, economic benefit rather than religious conversion were paramount, and missionary efforts avoided predominantly Muslim areas such as Java. The Dutch East India Company (VOC) regulated the missionary work so it could serve its own interests and focused it to the eastern, Animist part of the archipelago, including Maluku, North Sulawesi, Nusa Tenggara, Papua and Kalimantan. Christianity later spread from the coastal ports of Kalimantan, and missionaries arrived among the Torajans on Sulawesi. Parts of Sumatra were also targeted, most notably the Batak people who are predominantly Protestant today.