The Central Asian Republic of Tajikistan is eager to align its system of higher education with the European model. Recently, there have been significant policy pronouncements related to joining the Bologna Process and visible efforts to incorporate the European academic degree structure and credit hour systems. Meanwhile, university autonomy and academic freedom that Western universities historically enjoy and that the Bologna Process strongly supports and encourages do not seem to be embraced in the transformation of Tajik universities. The terms “university autonomy” and “academic freedom” do exist in policy documents. Their definitions and meanings, however, are seriously confused. This article investigates concepts of university autonomy and academic freedom in Tajikistan at both the national and university levels, comparing them with Bologna concepts. We analyze Tajik education laws and university statutes related to university autonomy and explore how universities currently conceptualize and act upon developing university autonomy and ensuring academic freedom that the republic professes to embrace. Also, based upon observation and ethnographic interviews in several universities in 2011–2012, we briefly discuss faculty and administrative perceptions of university autonomy and academic freedom and the extent to which these are experienced “on the ground.”