Women's academic careers are shorter, slower, and progress less than those of men. We investigated gender differences in thinking about leaving an academic career across career stages. Our analysis of data from an online survey of academics in the Czech Republic (1657 individuals) showed that in men, the trajectory of such considerations gradually decreases after obtaining a Ph.D. (except for 6-10 years post-Ph.D.), while in women it starts to drop significantly only after earning associate professorship and even then the decrease is less steep than for men. In both men and women, differences in thoughts of leaving across career stages were explained mostly by biological age and salary but in women, leadership position was also an important factor. Surprisingly, neither in men nor in women were differences in thinking about leaving explained by job satisfaction. Our findings imply that for women, achievement of a leadership position is more important with respect to thoughts of leaving than for men and that career age is for women less important than academic rank. We suggest that gender differences in trajectories of thinking about leaving may be linked to different perceptions of career prospects, especially at the career stage of 11 + years post-Ph.D.