A resident of Nagasaki, Yamaguchi was in Hiroshima on business for his employer Mitsubishi when the city was bombed on 6 August 1945. The following day he returned to Nagasaki and, despite his wounds, returned to work on 9 August, the day of the second atomic bombing.
Yamaguchi lived and worked in Nagasaki, but in the summer of 1945 he went to Hiroshima for a three month business trip. On 6 August he was preparing to leave the city with two colleagues, Akira Iwanaga and Kuniyoshi Sato, and was on his way to the station when he realized he had forgotten his hanko, and returned to his workplace to get it. At 8:15 he was walking back towards the docks when the American bomber Enola Gay dropped the Little Boy atomic bomb near the centre of the city, only 3 km away. Yamaguchi recalls seeing the bomber and two small parachutes, before there was "a great flash in the sky, and I was blown over" The explosion ruptured his eardrums, blinded him temporarily, and left him with serious burns over the left side of the top half of his body. After recovering he crawled to a shelter, and having rested he set out to find his colleagues. They had also survived and together they spent the night in an air-raid shelter before returning to Nagasaki the following day. In Nagasaki he received treatment for his wounds and, despite being heavily bandaged, he reported for work on 9 August.
At 11 am on August 9, Yamaguchi was describing the blast in Hiroshima to his supervisor, when the American bomber Bocks Car dropped the Fat Man atomic bomb onto Nagasaki. His workplace again put him 3 km from ground zero, but this time he was unhurt by the explosion.