The temple compounds date from the 8th to 9th century CE, linked with historic Mataram Kingdom that ruled Central Java during that period.

Prambanan however, was the latest addition in the complex, finished and inaugurated in 856 during the reign of King Pikatan according to Shivagrha inscription.

For centuries later, it fell into disrepair, buried under Mount Merapi volcanic debris and shaken by earthquakes.

In 1918, the Dutch colonial government began the reconstruction of the compound, and proper restoration took place in 1930 with modest result due to loss of the temple stones.

Only a number of the smaller pervara shrines of Prambanan and Sewu complex were reconstructed during the Dutch East Indies period prior to the Pacific War.

The reconstruction of the main Shiva temple in Prambanan complex was completed around 1953 and inaugurated by Indonesia's first president Sukarno.

Archaeologists believe the original name for the temple compound to be Manjusrigrha, which means "the house of Manjusri", one of the major Bodhisattva in Mahayana Buddhism belief.