The Japanese economy embarked in the last decades of the 19th century on a process of innovation leading to an acceleration of economic growth. As available estimates of national accounts (Ohkawa and Shinohara 1979) provide only country level figures starting in 1885, the distinctive features of the early phase of Japanese economic development remain a matter of debate and conjecture. Relying on new sectorial GDP and labour productivity estimates for 1874, 1890, and 1909, for each of the 47 prefectures (Fukao et al. 2015), we conduct a quantitative analysis of structural change during Meiji Japan's economic miracle, accounting also for its regional dimension.