It was built around 850 CE by either Rakai Pikatan, king of the second Mataram dynasty, or Balitung Maha Sambu, during the Sanjaya Dynasty. Not long after its construction, the temple was abandoned and began to deteriorate. Reconstruction of the compound began in 1918. The main building was completed in around 1953. Much of the original stonework has been stolen and reused at remote construction sites. A temple will only be rebuilt if at least 75% of the original stones are available, and therefore only the foundation walls of most of the smaller shrines are now visible and with no plans for their reconstruction.

The temple was damaged during the earthquake in Java in 2006. Early photos suggest that although the complex appears to be structurally intact, damage is significant. Large pieces of debris, including carvings, were scattered over the ground. The temple has been closed to the public until damage can be fully assessed. The head of Yogyakarta Archaeological Conservation Agency stated that: "it will take months to identify the precise damage".[2] However, some weeks later in 2006 the site re-opened for visitors. As of 2009, the inside of most temples still remains off-limits for safety reasons.

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