He graduated from the 14th class of the Imperial Japanese Army Academy in 1903, and his classmates included future generals Motoo Furushō and Toshizō Nishio.

He graduated from the 24th class of the Army Staff College in November, where his classmates included Kenji Doihara, Kiyoshi Katsuki, Hisao Tani, and Yanagawa Heisuke.

He quickly advised Imperial General Headquarters that it would be impossible to hold the border with the Soviet Union with the forces allocated, as the Kwantung Army had largely been hollowed out with redeployment of experienced troops (with most of their equipment) to the Pacific theater of the war.

However, when the Soviet Army invaded Manchuria on 9 August 1945, many of Yamada's makeshift forces were no more than 15% combat ready and were quickly overrun.

During his trial, he admitted to authorizing the use of "Ishii bombs", fragile porcelain grenades containing typhus and bubonic plague bacteria, which had been developed by Unit 731 for use in bacteriological warfare.

Yamada was also found to have presided over and encouraged biochemical weapon experimentation on involuntary human subjects, resulting in the torture and murder of thousands of people.