Saitama Prefecture is bordered by Tokyo, Chiba, Ibaraki, Tochigi, Gunma, Nagano, and Yamanashi. It is located central-west of the Kanto region, measuring 103 km from east to west and 52 km from north to south. At 3,797 km2, it ranks as the ninth smallest prefecture. The eastern border with Chiba Prefecture is defined by the Edo River. The northern and north-western border lines with Gunma Prefecture are marked by the Tone River and the Kanagawa River and the drainage divides of the Arakawa River and Kanagawa River. The southwestern border is defined by the drainage divides of the Arakawa River, Tama River, and Fuefuki River. The eastern section of the southern border line, however, does overlap with any geological feature.

The topography of Saitama Prefecture is largely divided by the Hachioji Tectonic Line, which runs through Kodama, Ogawa, and Hanno, into the western mountain area and the eastern lowland area. The altitude, highest on the western side, gradually lowers eastward from mountain ranges to hills to plateaus to lowlands. The eastern lowlands and plateaus occupy 67.3 % of the area.

The eastern side, part of the Kanto Plain, can be further divided into nine separate expanses of hills and ten plateaus. The former occupy small areas neighboring the Kantô Mount Range, including the Hiki Hills and Sayama Hills. The latter are mainly surrounded by alluvial flood plains. In the southeastern portion of the prefecture, the Omiya Plateau stands in a southeastward direction, sandwiched by the Furutone River to the east and the Arakawa River to the west.

The western side of the prefecture belongs to the Kanto Mountain Range with Chichibu Basin located in its center. The area to the west of the basin features high peaks such as Mount Sanpo (2,483 m) and Mount Kobushi (2,475 m), in which the Arakawa River has its source. Most of the land is contained in Chichibu Tama Kai National Park. The area to east of the basin consists of relatively low mountains.