In the Russo-Japanese War, he captured Port Arthur but he felt that he had lost too many of his soldiers, so requested permission to commit suicide, which the emperor refused.

After completing the training, he was reassigned to the Kawatō Barrack in Kyoto as an instructor, and then as Toyōra domain's Army trainer in charge of coastal defense troops.

The next year (1876), Nogi was named as the Kumamoto regional troop's Staff Officer, and transferred to command the 1st Infantry Regiment, and for his service in the Satsuma Rebellion, against the forces of Saigō Takamori in Kyūshū, he was promoted to lieutenant colonel on April 22, 1877.

[6] In 1894, during the First Sino-Japanese War, Major-General Nogi commanded the First Infantry Brigade which penetrated the Chinese defenses and successfully occupied Port Arthur in only one day of combat.

[9] Advancing slowly down the Liaodong Peninsula, Nogi encountered unexpectedly strong resistance, and far more fortifications than he had experienced ten years earlier against the Chinese.

However, in an unprecedented action, Emperor Meiji spoke out during the Supreme War Council (Japan) meeting, defending Nogi and demanding that he be kept in command.

He led his Third Army against the Russian forces at the final Battle of Mukden, ending the land combat phase of operations of the war.

His second son Yasunori (December 16, 1881 – November 30, 1904), a second lieutenant at Port Arthur, fell on a rocky slope, striking his head and dying instantly.

When explaining battles of the Siege of Port Arthur in detail, he broke down and wept, apologizing for the 56,000 lives lost in that campaign and asking to be allowed to kill himself in atonement.

Emperor Meiji told him that suicide was unacceptable, as all responsibility for the war was due to imperial orders, and that Nogi must remain alive, at least as long as he himself lived.

[12] After the war, Nogi was elevated to the title of count and awarded the Order of the Rising Sun with Paulownia Flowers, Grand Cordon, 1907.

[13] Nogi spent most of his personal fortune on hospitals for wounded soldiers and on memorial monuments erected around the country in commemoration of those killed during the Russo-Japanese War.

Nogi and his wife Shizuko committed suicide by seppuku shortly after the Emperor Meiji's funeral cortege left the palace.

In either case, Nogi's suicide marked the end of an era, and it had a profound impact on contemporary writers, such as Mori Ōgai, Kuroiwa Ruikō and Natsume Sōseki.

The epic historical novel Saka no Ue no Kumo portrays Nogi as floundering at the Siege of Port Arthur and having to be relieved by Kodama Gentarō.

[17] Right after the Battle of Nanshan of 1904, in which he lost his eldest son, he wrote: 十里風腥新戰場 征馬不前人不語 金州城外立斜陽 For ten li, the foul odor of blood drifts on the wind over new battlefields.

In the NHK television adaptation of Ryōtarō Shiba's epic Saka no Ue no Kumo, which aired from 2009 to 2011, Nogi was portrayed by actor Akira Emoto.

In the manga and NHK television adaptation of Monster, General Nogi is mentioned by the Turkish elder and community leader, Mr. Deniz, convincing the others to trust Dr. Kenzo Tenma and a local prostitute when they attempt to convince the leaders of Frankfurt's Turkish Quarter to be wary of an imminent arson attack by neo-Nazis, led by The Baby.

Deniz makes reference to an incident wherein General Nogi saved an Ottoman fleet of the Turkish Navy that had run aground in the Pacific.