After graduation in 1874, Yamamoto went on a training cruise to Europe and South America aboard Imperial German Navy vessels from 1877 to 1878, and as junior officer acquired much sea experience.

He wrote a gunnery manual that became the standard for the Imperial Japanese Navy and served as executive officer of the cruiser Naniwa on its shakedown voyage from Elswick to Japan (1885 to 1886).

After serving as captain of the corvette Amagi, he accompanied Navy Minister Kabayama Sukenori on a trip to the United States and Europe that lasted over a year (1887 to 1888).

As Minister of the Navy during the Russo-Japanese War, Yamamoto showed strong leadership and was responsible for appointing Tōgō Heihachirō as commander-in-chief of the Combined Fleet.

However, his administration was plagued by charges of corruption and he was forced to resign with his entire cabinet in April 1914 to take responsibility for the Siemens-Vickers Naval Armaments scandal, even though it was never proved that he was personally involved.

However, he and his cabinet were forced to resign again in January 1924, this time over the attempt by Namba Daisuke to assassinate Prince Regent Hirohito on 27 December 1923 (the Toranomon Incident).

Suggestions that he be made one of the Genrō were vehemently opposed by his life-long political enemy, Saionji Kinmochi, who also blocked all efforts for him to have a seat on the Privy Council.

In December 1933, nine months after the death of his wife, Yamamoto died of complication due to benign prostatic hyperplasia at his home in Takanawa, Tokyo at the age of 82.