Gender balance across different employment sectors is beneficial in order for society to make the best use of its talent pool. However, particularly in the STEM (science, technology, engineering and mathematics) fields, women are underrepresented as researchers and professors in universities and non-university research organizations in Germany. To better understand the career trajectories of doctoral degree holders, we investigate the critical phase of transition into the post-graduation employment context. Based on rich process-generated data for a large German technical university, we explore the relationship of employment sector and employment volume during and after doctoral training. Results of a sequence analysis indicate that the employment trajectories of men and women follow similar patterns, but that the prevalence of individual sequences differs substantially by gender. Our findings suggest substantial path dependence in employment biographies. Regression results show no overall gender-specific difference regarding the post-graduation employment sector when controlling for previous sector-specific work experience and STEM subfields. However, when distinguishing between men, women without children and women with children (mothers), we observe that mothers are more likely to remain in the university sector compared to men. In the years following doctorate completion, both women without children, and women with children are significantly less often full-time employed than are men.