Under pressure from British ambassador Sir Harry Parkes to fulfil its obligations to make the waters and harbors of Japan safe for shipping, the Japanese government hired the Edinburgh-based firm of D. and T. Stevenson to chart coastal waters and to build lighthouses where appropriate. The project had already begun under French foreign advisor Léonce Verny, but was not proceeding fast enough for the British.

Brunton was sent from Edinburgh in August 1868 to head the project after being recommended to the Japanese government by the Stevensons, and over seven and a half years designed and supervised the building of 26 Japanese lighthouses in the Western style, along with two lightvessels. (There had been Japanese lighthouses before then, but they were short and squat buildings, such as the old Shirasu lighthouse now in the grounds of Kokura castle in Kitakyushu.) Brunton was accompanied by his wife and two assistants.

The old pre-Brunton Shirasu lighthouse in the grounds of Kokura Castle Brunton also established a system of lighthouse keepers, modeled on the Northern Lighthouse Board in Scotland.

He was consulted on other engineering projects, and significantly contributed to the waterworks and harbour design in Yokohama, where he is remembered by a commemorative statue. He also helped found Japan's first school of civil engineering.

Brunton wrote a memoir of his time in Japan, titled Pioneer Engineering in Japan: A Record of Work in helping to Re-Lay the Foundations of Japanese Empire (1868-1876). However, it was not published until the 1990s, when it was printed by separate publishers under two different names: Building Japan 1868-1876 and Schoolmaster to an Empire: Richard Henry Brunton in Meiji Japan, 1868-1876.