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Many studies report persistent inequalities between male and female employees on the labour market. Inequalities in temporal autonomy, i.e. freedom in the organisation of their paid working time, however, remain under-investigated. Using the 2013, 2016 and 2019 Working Conditions surveys and 38 interviews conducted between 2019 and 2021 with French employees, this article examines gender differences in time autonomy and their determinants. All else being equal, employed women are less likely to be able to change their working hours, to freely take time off and to endure attendance control. These differences can stem from employers treating men and women differently, or men and women having different preferences prior to entering the labour market. When these preferences are controlled for, time autonomy evolves differently for men and women through family and work changes, and mothers rather than fathers are encouraged to juggle work and family demands. This reiterates women’s association with the domestic sphere and men’s with the professional sphere.