Information on the safety of paternal use of medications prior to the time of conception is limited, and there is little available evidence regarding possible adverse effects of paternal use of systemic corticosteroids (SCS). In this cohort study, based on nationwide data, we examined the association between paternal use of SCS prior to conception and adverse birth outcome. The study includes data from all singletons born in Denmark from 1 January 1997 through 2013 (N = 1,013,994). Children fathered by men who redeemed a prescription of SCS within 3 months before conception (N = 2380) constituted the exposed groups. The outcome was congenital abnormalities (CAs), pre-term birth and small-for-gestational age (SGA). We adjusted for co-variates in multi-level logistic regression analyses. The adjusted odds ratios for pre-term birth and SGA were 0.81 (95% CI: 0.55-1.21) and 1.06 (95% CI: 0.68-1.64), respectively. The adjusted odds ratios for CAs were 1.08 (95% CI: 0.87-1.40) in children fathered by men who redeemed one prescription within 3 months before conception and 1.33 (95% CI: 0.99-1.79) in children fathered by men who redeemed two or more prescriptions. This study is the largest to date examining the effect of paternal use of SCS prior to conception on birth outcome. We found no significantly increased risk of pre-term birth or SGA. In children of fathers who redeemed at least two prescriptions of SCS within 3 months before conception, we found an increased risk of CAs, though not statistically significant. The types of CAs did not show a distinct pattern.