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Born to a village physician's family in Suo Province (present-day Yamaguchi Prefecture), he studied Dutch learning and medicine at Ogata Koan's Tekijuku in Osaka and went on to study Western medicine and military science from Siebold in Nagasaki, serving the Uwajima domain and the shogunate in military studies and translation. He supported Takasugi Shinsaku's Kiheitai in Choshu and effectively commanded the Choshu forces in the Shimonoseki War of 1866, repelling the shogunate armies. In the Boshin War he served as the de facto supreme commander of the imperial forces, directing battles across the country and demonstrating his military genius to the full. In the new Meiji government, as Vice-Minister of Military Affairs he built the foundations of a modern military system, promoting nationwide conscription and Westernization of the army. However, he incurred the resentment of traditional samurai forces, and on September 4, 1869, he was stabbed in Kyoto by former Choshu samurai; he died on November 5 at the age of forty-five. A bronze statue of Omura stands at the entrance of Yasukuni Shrine (Kudan, Tokyo), honoring him as the founder of the modern Imperial Japanese Army. The career of a physician trained by Ogata Koan who built the military system of a nation symbolizes the diversity of talent in Bakumatsu Japan.

A straightforward, single-minded man devoted purely to scholarship and practice. He valued ability regardless of status or origin, and his firmness in not yielding to old authority provoked resentment. As his starting point as a physician shows, his dedication to putting knowledge to use in society was consistent throughout his life.

He built the institutional foundations of the modern Imperial Japanese Army, laying the groundwork for the conscript army that Yamagata Aritomo and others inherited. As the first person to have a bronze statue erected at Yasukuni Shrine, he is a symbolic figure standing at the starting point of Japan's modern military history.