Harootunian edited volumes on 20th-century politics in Japan, but is best known for a series of wide-ranging monographs on the development of Japanese social and intellectual thought from late Tokugawa period through the middle of the 20th century.

He was Editor, Journal of Asian Studies, Coeditor, Critical Inquiry, and with Rey Chow and Masao Miyoshi, co-edited the Asia-Pacific series for Duke University Press.

Pyle adds that “this is not an easy book” but the approach to intellectual history is “nonetheless intelligent and imaginative.”[2] Things Seen and Unseen: Discourse and Ideology in Tokugawa Nativism (1988) focuses on Kokugaku, which Harootunian translates as "nativist," a loosely related group that resisted Sinocentric, or Chinese, traditions and developed new frameworks which emphasized home-grown thought.

Yamashita added that this “is not, by conventional standards, a very readable book, but the puzzling and occasionally obtuse prose was partly intended" and that "readers unfamiliar with the issues being discussed and the theoretical material invoked will miss the main points of the book.”[3] Overcome by Modernity (2000) deals with the artists, critics, philosophers, poets, and social scientists of the 1920s and 1930s, a period when Japan had entered into the “heroic phase of capitalism.” They were caught in the dilemma of explaining why Japan had to overcome “modernity” while explaining why it could not.

Jeffrey Hanes of the University of Oregon, wrote in the American Historical Review, that “this is a formidable book” that is a “challenging sometimes maddening read, but one that rewards us with a terrifically insightful and poignant evocation of Japan’s attempts to come to grips with the modern world into which it was thrust and into which it then threw itself.” [4] Harootunian was a proponent of the movement to adapt and apply critical theory in a way that would put Japan in the same frame of analysis as other capitalist countries rather than making it exotic.

Lie's objection was that this approach put all Asian countries into one category, did not give enough weight to historical change, and did not place enough emphasis on class differences.

The volume Harutoonian edited with Masao Miyoshi in 2002, Learning Places: The Afterlives of Area Studies is a collection of essays that critically examine the rise of Area Studies during the Cold War, then analyze the late 20th century, post-Cold War "need of foreign governments, mostly outside Euro-America, to pay American universities and colleges to teach courses on their histories and societies."