The construction of Kubota Castle started in May 1603 and was completed in August of the same year. With no donjon, which is a symbolic icon of other Japanese castles, nor stone walls, this castle was mostly made of mounds and wooden fences.
The hon-maru (main building) was in the shape of a rectangle, 117 meters wide east-west and 216 meters long north-south, located on a concave surface dug out of Mt. Shimmei at its peak. The ni-no-maru (second building) was in the shape of a strip, 70 meters wide east-west and 432 meters long south-north, on low-lying land to the east of the hon-maru. The san-no-maru (third building) and kita-no-maru (north building) were placed around the hon-maru and ni-no-maru.