Aims: Employee-based flexible working hours are increasing, particularly among knowledge workers. Research indicates that women and men use work–time control (WTC; control over time off and daily hours) differently: while men work longer paid hours, women use WTC to counteract work–life interference. In a knowledge-worker sample, we examined associations between WTC and overtime, work–life interference and exhaustion and tested whether gender moderates the mediating role of overtime. Methods: The sample contained 2248 Swedish knowledge workers. Employing hierarchical regression modelling, we examined effects of control over time off/daily hours on subsequent overtime hours, work–life interference and exhaustion in general and in gender-stratified samples. Using conditional process analysis, we tested moderated mediation models. Results: Control over time off was related to less work–life interference (β_men= −0.117; 95% confidence interval (CI): −0.237 to 0.003; β_women= −0.253; 95% CI: −0.386 to −0.120) and lower exhaustion (β_men= −0.199; 95% CI: −0.347 to −0.051; β_women= −0.271; 95% CI: −0.443 to −0.100). For control over daily hours, estimates were close to zero. While men worked more overtime (42 min/week), we could not confirm gender moderating the indirect effect of control over time off/daily hours on work–life interference/exhaustion via overtime. Independent of gender, effects of control over time off on work–life interference were partly explained by working fewer overtime hours. Conclusions: Control over time off was related to lower exhaustion and better work–life balance (in particular for women). We found no evidence for men’s work–life interference increasing with higher WTC owing to working more overtime. Knowledge workers’ control over time off may help prevent work–life interference and burnout.