What does it mean to be an atheist in Japan and what do the Japanese understand to be the difference between being non-religious and being atheist? When and under what conditions do such questions become relevant for the Japanese to consider? In order to answer such questions, one must go back to a time and place where the Japanese begin to consider atheism as a cultural concept. This work explores the topic of intellectual atheism as both product and agent of sweeping cultural changes in a rapidly modernizing Meiji Era Japan. It considers the influences of various social forces upon traditional modes of living and thinking as well as the response of these forces to challenges presented by modernization and by the enduring aspects of traditional Japanese life. The essay addresses these historic events through the lens of the agents of these social forces and examines their influence and legacies with regard to various aspects and institutions of Japanese life including politics, education, research, economics, and religious traditions in modern Japan.