Postwar relations between Indonesia and Japan started with war repatriations payments from Japan to Indonesia in 1958, and have progressed to include Japanese investment and business expansion into Indonesia, Official Development Assistance programmes and the flow of Japanese popular culture to Indonesia. What connects these relations are their patron–client characteristics, with Japan tending to give while Indonesia tends to receive. This also evident in Japanese Studies programmes in Indonesian higher education institutions, which developed relying heavily on support from Japan. Such dependency, combined with fascination regarding ‘Japanese culture’, has resulted in the pervasive existence of academic ‘Japanese hegemony’. Concerns regarding this tendency have risen among scholars in Indonesia, highlighting the urgency to maintain balance in the relationship between Indonesia and Japan within academic contexts, and to incorporate insights from Indonesia into the study of Japan. It is in this spirit that critical thinking skills began to be adopted in the curricula of Japanese Studies programmes in Indonesian higher education institutions. By focusing on the curricula of two Japanese Studies programmes, at Universitas Indonesia and Universitas Airlangga, this chapter portrays recent trends in Japanese Studies in Indonesian higher education institutions.