Just north of the Bayon is the stalwart form of the Baphuon, a temple mount built in 1066 and an important Khmer capital. Early French archaeologists sought to restore the crumbling mount, and began to disassemble the temple block by block, but their efforts were interrupted by war, and it would be some years before archaeologists would return to find a confused jigsaw puzzle of a dismantled temple. The plans were lost. Bilateral efforts are underway to solve the puzzle and put the temple back together, and these ongoing efforts give visitors an idea of what original temple construction might have been like. The Baphuon was the last capital in the Angkor period.

The east gate of the Baphuon is the only remaining part of what was once a large laterite wall. A narrow causeway with moats on either side connects the gate with the main temple. The temple has five levels that are all the same height, which makes the site more like a pyramid and quite unique among Angkor temples. Note: From the Baphuon you can make a clockwise loop, first to Vimean Akhar, then to the Terrace of the Leper Kings and the Terrace of Elephants (all on foot) before you return to the vendors' area and your awaiting chariot to go on to Preah Khan or via the east gate to Ta Prohm.