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Background The effect of long working hours on mental health has drawn great social attention in recent years. Aims We investigated how work–family conflict mediates the associations between long working hours and sleep disturbance and burnout. Method We included 19 159 individuals from a nationally representative sample of workers in South Korea. We decomposed the total effect into a direct effect (long working hours → sleep disturbance or burnout) and an indirect effect (long working hours → work–family conflict → sleep disturbance or burnout). Logistic mediation models were used. Results Long working hours were associated with increased risks of work–family conflict, sleep disturbance and burnout. The longer the working hours, the stronger the direct and indirect effects. The odds ratios of the direct effects of long working hours on sleep disturbance were 1.64 (95% CI 1.39–1.95) for 49–54 h/week and 1.66 (95% CI 1.37–2.01) for ≥55 h/week; those of the indirect effects were 1.16 (95% CI 1.12–1.21) for 49–54 h/week and 1.27 (95% CI 1.21–1.33) for ≥ 55 h/week. Similarly, odds ratios of the direct effects of long working hours on burnout were 1.18 (95% CI 1.05–1.33) for 49–54 h/week and 1.20 (95% CI 1.04–1.37) for ≥55 h/week; those of the indirect effects were 1.11 (95% CI 1.09–1.15) for 49–54 h/week and 1.20 (95% CI 1.16–1.24) for ≥55 h/week. Conclusions Our results suggest that work–family conflict mediates the associations between long working hours and sleep disturbance and burnout. Longitudinal studies should be followed to confirm the causal relationship.