With its ostensibly liberal-democratic institutions and constitutional safeguards for civil liberties, Japan might be expected to stand as a beacon of academic freedom in East Asia. Indeed, while global trends relating to the corporatization of higher education have made significant inroads in Japan as elsewhere, a strong tradition of faculty autonomy has so far helped limit their impact here. However, this paper argues that the scope and influence of scholarly debate are significantly constrained by factors both internal and external to universities. A longstanding and extreme bias in public policy (and funding priorities) toward the “hard” sciences has recently worsened, exacerbating the marginalization of social sciences and humanities within the academy. Media freedom also faces concerted attack from right-wing political forces, which have simultaneously sought to pressure scholars conducting critical research on “sensitive” issues – especially relating to Japan’s wartime past. And while faculties strive to fend off external interference, their own composition reflects a narrowness and lack of openness in Japanese academia. With women and foreigners still marginalized, questions arise as to whose autonomy is to be valued and defended and for what purposes. Drawing on a range of sources in Japanese and English, as well as the author’s own experience as a researcher based in Japan, this chapter highlights some of the tensions or contradictions in current debates over academic freedom and assesses the prospects for the development of a more outward-looking, politically engaged academic culture.