Its architectural style is very similar to that of the earlier East Mebon, the major difference being the stepped pyramid of the Pre Rup that is missing in the East Mebon temple. The laterite and brick structure represents the five mountain peaks of the sacred mountain Mount Meru, the center of the universe in Hindu mythology.
An inscription in the temple mentions that the five prangs were dedicated to Shiva (central tower and one of the surrounding towers), Vishnu, Parvati (the consort of Shiva) and Lakshmi (the consort of Vishnu).
The temple used to be surrounded by moats. There are two enclosures, each with a gopura entrance gate at the center of each side. Between the outer and inner enclosure were long halls of which not much remains today. They were a predecessor of the galleries seen in later temples.
Most striking feature of the Pre Rup temple are the three large towers on either side of the Eastern entrance, the main entrance of the temple. The first tower to the right of the entrance is missing, although the base is there. The tower was either never build or demolished and the stones used elsewhere later. The towers were probably build later during the reign of the next King, King Jayavarman V.
The central tower contains a sanctuary room. The lintels contain Indra riding the elephant Airavata, Vishnu on Garuda (a large mythological bird, the mount of Vishnu) and other depictions.
The inner enclosure contains a three tiered pyramid. On the pyramid’s second level are 12 small sanctuaries grouped around the structure that each used to contain a linga, a representation of Shiva. At the center of each side of the pyramid is a stairway leading to the platform with the five towers. The stairway is guarded on both sides by lion statues.