In the last few decades, the percentage of women graduating in medicine has increased gradually in North America and in Europe [1, 2]. With this process of “feminisation” of medicine, various aspects such as the clustering of female and male physicians in different specialties, salary inequalities, working hours preferences and implications for the practice of medicine and for patients were observed [3–5]. However, at the same time a “leaky pipeline” was identified within the academic track of medicine: the underrepresentation of women at higher professorial levels and leadership positions in medical faculties [1, 6]. Unlike the progress observed in other disciplines, such as humanities and social sciences, with a similar feminisation trend, in medicine advances have been described as “incomplete and inadequate” [6]. In 2013 to 2014 in the US, women represented almost half of all matriculants (47%) [1]. However, at the faculty level finally only 38% were women with 21% full women professors [1]. The contrast is even more striking in Switzerland: women made up 61% of students in 2014, but represented only 17% of professors [7, 8]. Within this highly gender unequal context, measures promoting female faculty seem particularly needed in Switzerland. This article addresses efforts to combat women's underrepresentation in leading academic medicine positions by describing and analysing the action plans implemented within the faculties of four of the largest Swiss universities: Basel, Geneva, Lausanne and Zurich. Geneva and Lausanne represent faculties of the French-speaking part of Switzerland, whereas Basel and Zurich are located in the German-speaking part. After describing the obstacles to women's advancement in leadership positions in medicine identified in the research literature, the article presents the main theoretical approaches adopted to counter these inequalities. We then present the case studies of the four Swiss faculties of medicine where action plans were implemented within the frame of the Swiss Federal Equal Opportunity at Universities Program, which ran from 2013 to 2016. Focusing on the innovative faculty-based actions undertaken, we discuss the advantages of combining strategies that empower women with those that change institutions by modifying their structure and culture to advance gender equality.