The aim of this article is to examine the effect of New Public Management (NPM) inspired universityhuman resource management (HRM) practices on gender segregation at universities. Drawing on gender and organisational theories, we conducted a case study of a managerial university in Lithuania drawing on analyses of policy documents, websites and senior academic staff survey data (n=142). We find vertical gender segregation in the management structures of the case study university, with women academics being more likely to experience career progression barriers than men. This study contributes to higher education, gender and management research in three important ways: (1) by providing empirical evidence of the persistence of gender segregation at a university, despite the transformation of university HRM practices, (2) by providing a more nuanced picture regarding gender and tokenism among university management, (3) by pointing out that despite the long tradition of women employment in the post-Soviet Central and Eastern European context, universities are still the bastions of the masculine culture and power, where women academics face a ‘glass ceiling’ to reach management positions. We discuss the practical implications for gender-balanced composition of higher education management at Lithuanian universities.