Born in 1847 in Kagoshima as the fifth son of the Satsuma samurai Mori Arinori. He studied English at the domain's Western-learning school Kaiseijo, and in 1865 on domain orders stowed away with Godai Tomoatsu and others to study in Britain. He studied at University College London and also crossed to America, where he spent time at a Christian commune. After the Restoration he served as a foreign affairs judge in the new government, then went to the United States as Japan's chargé d'affaires. In 1875 he founded the Commercial Training Institute (Shoho Koshujo) in Tokyo — forerunner of Hitotsubashi University. Known as a radical Westernizer, he even argued for making English the national language. In 1885 he became Japan's first Minister of Education under Ito Hirobumi's cabinet and promulgated as a single system the Elementary School, Middle School, Imperial University, and Normal School Ordinances, thereby designing the modern Japanese school system. His statist view of education, 'education for the sake of the nation,' is also a notable feature. On February 11, 1889, the very day of the promulgation of the Meiji Constitution, the ultranationalist Nishino Buntaro stabbed him with a short sword, citing 'impiety' at Ise Shrine, and he died the next day. He was 42.

A rationalist and a man of action. Never averse to breaking with old customs, he pressed reform and went so far as to argue for abolishing Japanese and adopting English — an extreme Westernizer. At the same time, in designing the school system he displayed meticulousness, systematically ordering regulations, examinations, and teacher training. A confident man with many enemies, but the skeleton of Meiji education sprang from his conceptions.

The systematic school structure Mori designed — from elementary school through the Imperial University — formed the foundation of Japanese education down to the postwar reforms. The Shoho Koshujo became Tokyo University of Commerce and eventually Hitotsubashi University, sending many talents into the Japanese business world. His statist view of education, on the other hand, opened the way to the Imperial Rescript on Education (1890), so that he is assessed as a man who — for good and for ill — decisively shaped modern Japanese education.