Before the present Jagannath Temple was built, the site at Jagannath Temple known in ancient times as Purushottama Kshetra or Nilachala—was already an important Hindu pilgrimage centre. Ancient Hindu scriptures, including the Skanda Purana, Narada Purana, and Matsya Purana, describe Purushottama Kshetra as a sacred place dedicated to Lord Vishnu. The 11th-century Sanskrit work Prabodha Chandrodaya Nataka by Krishna Mishra also refers to a temple (devayatana) of Purushottama, showing that a shrine existed before the construction of the present temple. Traditional accounts also state that Adi Shankaracharya visited Puri during the 8th–9th century CE and established the Govardhan Math, confirming that Puri was already a major centre of pilgrimage before the 12th century.

The present Jagannath Temple was rebuilt in the early 12th century CE by Anantavarman Chodaganga of the Eastern Ganga dynasty, who ruled from approximately 1078 to 1150 CE.

Originally a devotee of Lord Shiva (Shaivite), Anantavarman later embraced Vaishnavism after conquering the Utkala region in 1112 CE. Historical inscriptions show that he donated to the temple in 1134–1135 CE, indicating that construction had begun after 1112 CE.

His successor, Anangabhima III (r. c. 1211–1238 CE), dedicated the entire kingdom of Utkala to Lord Jagannath and referred to himself as the "Rauta" (servant) of the deity rather than the king.

During the 15th and 16th centuries, the Gajapati kings of Odisha, especially Kapilendra Deva and his successors, greatly expanded the temple's importance. Under their patronage, the Jagannath Temple became one of India's foremost religious and cultural institutions and the spiritual center of the Gajapati kingdom.

In 1568 CE, after the defeat of Gajapati king Mukunda Deva, the Afghan general Kalapahad invaded Puri and attacked the Jagannath Temple. According to the Madala Panji (the temple chronicle), the temple treasury was looted, and the wooden idols of Lord Jagannath, Balabhadra, and Subhadra were damaged and burned.

Temple tradition states that Bisara Mohanty rescued the sacred Brahma Padartha (the divine essence) from the damaged idol and preserved it.

Later, Ramachandra Deva I restored the temple, commissioned new wooden idols, and reinstalled the deities in 1575 CE. This restoration is regarded as the first Nabakalebara ceremony, in which the sacred wooden idols are ceremonially renewed.

During the Mughal period, the Jagannath Temple faced repeated invasions and political pressure. Several Mughal governors and military commanders attacked or occupied Puri.

According to the Madala Panji, the temple was attacked and plundered 18 times. To protect the deities, temple servitors secretly moved them to safe locations around Chilika, Khurda, Banpur, Kodala, and nearby regions until it was safe to return.

After the British East India Company conquered Odisha in 1803, it took over the administration of the Jagannath Temple.

Initially, the temple was managed by a government-appointed board of Brahmins. In 1809, administration was transferred to the hereditary Raja of Khurda and his successors.

The British continued the pilgrim tax introduced during the Maratha period. The revenue funded temple maintenance, repairs, and improvements to pilgrimage routes, including the road connecting Puri and Calcutta (now Kolkata).

During British rule, Christian missionaries criticized government involvement in managing a Hindu temple and collecting pilgrim taxes. They argued that the British government should not support religious institutions.

In 1833, the British government decided to reduce its involvement in temple affairs. In 1840, the pilgrim tax was abolished. The Raja of Khurda continued to oversee the temple's internal administration, while the government gradually withdrew from direct management.

After India became independent in 1947, the administration of the temple was reorganized under state law.

The Puri Shri Jagannath Temple (Administration) Act, 1952 documented the temple's customs and traditions. Later, the Shri Jagannath Temple Act, 1955 established the present administrative system.

The Act came into force on 27 October 1960, placing the temple under the Shri Jagannath Temple Managing Committee, headed by the Gajapati Maharaja of Puri. Amendments made in 1983 continue to provide the legal framework for the temple's administration today.