Yamamoto is a fair-skinned man of average height. The oldest captain in the Gotei 13, he has aged into a elderly man with a bald head, visible wrinkles, hooked nose, and pronounced cheekbones. He has red eyes, long eyebrows, long mustache, and a hip-length white beard secured by a purple band crossing down it. He has many scars on his body, with the two most prominent being a pair of long scars crossing above his right eye, one of which was left by his battle with his lieutenant. In addition to the standard Shinigami uniform, he wears a captain's long-sleeved haori draped over his back instead of actually wearing it, with its size being greatly exaggerated. Despite his old and frail demeanor, often standing in a hunch, he in fact has a very muscular and well-defined built, which he only reveals when serious for battle, something which Shunsui Kyōraku claims is not seen too often. After his confrontation with Sōsuke Aizen, Yamamoto lost his left arm.

When he was much younger, Yamamoto had black hair on the sides of his head, and was bald on top. He had a tuft of hair sticking up at the back of his head in a topknot. He had thick but more manageable eyebrows and mustache with no beard. He had a single large scar on his forehead, which earned him the nickname "Eijisai" due to its shape. He had a prominent crease on his forehead and beneath his eyes, and shallow cheeks. He wore the typical black outfit of a Shinigami, with the addition of a sleeveless captain's haori worn appropriately.