Total anomalous pulmonary venous connection (TAPVC) is a rare and life-threatening condition, and long-term patient outcomes remain to be fully explored. This registry-based national cohort study including all Danish children born with TAPVC between 2000 and 2018 aimed to evaluate the survival rates of Danish children receiving a TAPVC repair procedure. Additionally, the prevalence of early morbidity, severe chronic diseases, and mental and/or behavioral disorders in children diagnosed with TAPVC was investigated using Danish health registries. A total of 89 children with TAPVC were identified, of whom 65 underwent primary repair. Among those receiving surgery, the survival rate was 88% at 3 months, decreasing to 78% at 20 years. In the cohort of children with a TAPVC primary repair, 26% had one or more hospital visits with primary or secondary chronic somatic diagnoses, and 8% had one or more hospital visits with a mental and/or behavioral disorder. In comparison, 6% of all Danish children born during the same period had similar hospital visits for somatic diseases, and 3% for mental and/or behavioral disorders. The survival rate of our TAPVC cohort aligns with that reported in the literature. Furthermore, this study highlights the need for additional research into the physical and mental health of these children, as they require hospital care more frequently than their peers.