Pueblo Pintado is L-shaped with a central room block and a west wing, but no east wing. The arc of rooms that encloses the plaza on the south continues to the east, thereby creating an east "side" to the structure. It covers less ground area than most canyon great houses but has slightly more rooms (135 total) than Pueblo Alto. The pueblo rose to three stories, and possibly four. Unlike most great houses, the plaza contains a large mound that probably represents the remains of a room block. A later Navajo corral was built southeast of the structure in the vicinity of a large trash mound.
Construction appears to have started at Pueblo Pintado in the 1060s and probably continued through the late 1000s. The site has not been excavated, and few tree-ring dates have been collected. A community of more than thirty small house sites encircles the great house. At least one Chacoan Road is present, the East or Pintado-Chaco Road, which begins near the southwest corner of the great house and runs west to the head of Chaco Canyon.
Pueblo Pintado is located about 2 miles off BIA Highway 9 via dirt roads that are un-numbered.