In Sweden, sickness absence due to mental disorder is increasing for both men and women, although more among women. The psychosocial work environment is acknowledged as an important predictor for sickness absence. Employee based work-time control is beneficial for the balance between job stress and recovery and could therefore be of interest when aiming to prevent sickness absence. The aim is to investigate the association between control over daily hours (CoDH) and control over time off (CoT), respectively, and sickness absence. The study also examine whether the association differ by gender and if burnout or depression mediates the associations. Data was derived from two waves of the Swedish Longitudinal Occupational Survey of Health (SLOSH) which is an approximate representation of the Swedish working population (n=8418, of which 4936 were females). Binary logistic regression was used as method of analysis. After adjustment for possible confounders, no association between CoDH and sickness absence was found. Low CoT was significantly associated with sickness absence among men (OR=0.90 [0.84, 0.96]), but not among women. Neither burnout nor depression mediates the associations. CoT is stronger associated with sickness absence than CoDH. CoT with regard to sickness absence is of greater importance for men than women.