The origin of this unusually shaped Pabalu Vehera stupa is unknown but it is believed to have been built by one of the king Parakramabahu's ( 1153-1186 AD) consorts, queen Rupawathi. The original name of this stupa is not known. The current name "Pabalu" (meaning beads) was derived from the fact that a large number of small glass beads were found during the excavation of the area around the stupa. The top part of the stupa has been destroyed by invaders and the center of the stupa also has been destroyed probably by treasure hunters in recent times.

Generally, Stupa's has only 4 image houses around it. But there are nine image houses around the stupa. These contain sitting images in some and standing images in others. One houses a "Sri Pathla" (the impression of the foot) of Buddha. Another one contains a Buddha statue in the reclining position. It is thought these image houses have been built at different time periods by different people. In addition, there is a stairway to reach the first level of the stupa.