Background. Decreased work ability due to mental disorders is a growing concern in Europe. We studied the role of work-family conflicts in association with long-term sickness absence due to mental disorders (LTSA-MD).Methods. Baseline data were extracted from the Helsinki Health Study for women aged 40 to 55 in full-time work in 2001 − 2002 (N = 2386). Questionnaire responses were linked with register data from the Social Insurance Institution of Finland on SA spells due to mental disorders during 2004–2010. We studied an overall question on satisfaction with combining work and family (WFS) and composite scores of work-to-family conflicts (WTFC) and family-to-work-conflicts (FTWC), and their components in association with the first certified SA spell (≥12 calendar days) due to a mental disorder during the follow-up. We performed Cox regression analyses with hazard ratios (HR) and their 95% confidence intervals (CI) adjusted for sociodemographic factors, work schedule, perceived mental and physical strenuousness at work, and self-rated health. First, we examined all participants, and second, only those who reported no prior mental disorder.Results. Poor work-family satisfaction (WFS) was associated with subsequent LTSA-MD, adjusting for all covariates (HR 1.60; 95% CI 1.10–2.16). Both high WTFC (1.64; 1.15–2.23), and high FTWC (1.43; 1.02–2.00) increased the probability of LTSA-MD in the full model. When participants with prior mental disorder were excluded, the association between poor WFS and WTFC with LTSA-MD retained while that between FTWC and LTSA-MD attenuated; however, two items of the FTWC were still associated with LTSA-MD: ‘Family worries and problems distract you from your work’and ‘Family matters prevent you from sleeping enough to do your job well’.Of the WTFC items, the following remained associated with LTSA-MD: ‘Problems at work make you irritable at home’and ‘Your job takes so much energy you do not feel up to doing things that need attention at home’.The experience of decreased time for work or family did not associate with LTSA-MD.Conclusions. Among female municipal employees, dissatisfaction with combining work and family and both work-to-family and family-to-work conflicts were associated with subsequent long-term sickness absence due to mental disorders.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-16075-y.