Purpose To examine whether family separation caused by prolonged waiting for family reunification is associated with the risk of mental disorders among refugee fathers. Method Based on full-population Danish registry data covering 1995-2015, we mapped arrival patterns among nuclear refugee family members resettled in Denmark (n = 76,776) and established a cohort of refugee fathers (n = 6176) who all arrived alone and later obtained family reunification with their wife and children. The fathers were followed for up to 24 years, from the day their residence permit was issued until their first psychiatric diagnosis, emigration, death, or study end, whichever came first. Using Cox proportional hazard regression, we estimated hazard ratios (HRs) of being diagnosed with a mental disorder (i) for the period while the fathers were still separated from their family and (ii) across varying lengths of family separation. Results The HR of any mental disorder was 2.10 (95% confidence interval (CI): 1.57-2.81) for fathers still separated from their family compared with those who had obtained family reunification. The HR increased with longer family separation. Compared with fathers separated for < 9 months, the HR of any mental disorder was 1.43 (95% CI 1.08-1.89) for 9-11 months' separation, increasing to 2.02 (95% CI 1.52-2.68) for 18-23 months' separation. Results were driven by post-traumatic stress disorder. Conclusion Fathers waiting for their wives and children face an increased risk of mental disorders. Countries receiving refugees should be aware that delaying family reunification can lead to adverse mental health effects.