Mori early developed an interest in Western studies, and in 1865 he was among the first Japanese to go abroad (to the University of London) for an education. He returned to Japan after the Meiji Restoration in 1868 and in 1870 was invited to join the new imperial government. He was appointed an investigator of parliamentary and educational systems and deputy minister to the United States.

In 1873 Mori, together with 15 other prominent intellectuals—including Fukuzawa Yukichi—formed the Meirokusha (“Sixth Year of Meiji Society”), to popularize Western ideas. Mori, one of the most vigorous westernizers of the group, wore Western clothing, engaged in ballroom dancing, and even advocated the writing of Japanese in the Latin alphabet.

After the Meirokusha was dissolved in 1875, Mori continued to serve in the new government, where he gained increasing influence. In 1885 he was appointed the first minister of education. As such, he helped develop a new centralized educational system, including an eight-year primary school program; a four-year middle school course; and higher levels of education up to and including a new national university. These schools not only educated the elite in Western subjects but also indoctrinated the general populace with Confucian ethics and patriotic fervour. Mori's iconoclasm, however, resulted in his death; he was assassinated by a religious fanatic after he allegedly desecrated the Ise Shrine, one of the holy places of the Shintō religion.