Myocarditis is associated with an increased risk of sudden cardiac death (SCD) in the young. However, information on nationwide burden of SCD caused by myocarditis (SCD-myocarditis) is sparse. For this study all deaths among persons in Denmark aged 1–35 years in 2000–2009 and 36–49 years in 2007–2009 (27.1 million person-years) were included. Autopsy reports, death certificates, discharge summaries, and nationwide registries were used to identify all cases of SCD-myocarditis. In the 10-year study period, there were 14 294 deaths, of which we identified 1 363 (10%) SCD. Among autopsied SCD (n = 753, 55%), cause of death was myocarditis in 42 (6%) cases corresponding to an SCD-myocarditis incidence of 0.16 (95%CI: 0.11–0.21) per 100 000 person-years. Males had significantly higher incidence rates of SCD-myocarditis compared to females with an incidence rate ratio of 2.2 (95%CI: 1.1–4.1). Myocarditis was not registered as cause of death in any of the non-autopsied SCD (n = 610, 45%). In conclusion, after nationwide unselected inclusion of 14 294 deaths, we found that 6% of all autopsied SCD was caused by myocarditis. No cases of SCD-myocarditis were reported in the non-autopsied SCD, which could reflect underdiagnosing of myocarditis in non-autopsied SCD. Furthermore, our data suggest a female protection towards SCD-myocarditis.