Inspired by New Public Management (NPM) and neoliberalism, higher education institutions (HEIs) are reshaping their governance and management systems. The shift from a collegial model to a ‘managerialist’ logic is reflected by the introduction of hierarchical management, higher accountability, and a focus on efficiency and performance indicators. Some studies have been emphasizing the complex relationship between the managerialist logic and gender relations in academia. Taking the case of two European countries recently influenced by managerialism and European policies to promote gender equality in HE—Portugal and Lithuania, this paper intends to analyse if the managerialist governance has been impacting the perceived influence- academics have in shaping the academic policies in their institutions and if there are gender differences on their perceptions on the influence over institutional decision-making processes in HEIs. Based on APIKS project, the findings indicate that performance-based management is positively associated with the academics’ influence in the institution. Moreover, the data suggest the more influential academics tend to be men in a higher academic rank. Furthermore, data analysis reveals that the new governance approaches re-emphasise the existing status quo in the sense that women perceive themselves as less influential than men and that the higher the institutional level of decision-making, the fewer women feel they have influence.