East Mebon was built on an island by Rajendravarman in the 10th century, the East Baray that surrounds the temple was built about 50 years before and was the second baray to be built by the ancient Khmer kings.

The temple was dedicated to the Hindu deity Shiva, and was built shortly after the capital was returned to Angkor from Koh Ker by Rajendravarman VII in the year 944 C.E. The approach to East Mebon is from the eastern side, what would have been a landing stage for boats now has wooden steps up to the temple.