Children with intestinal failure (IF) are at risk of loss of vascular access because of catheter-related venous thrombosis. Whether primary prophylactic anticoagulation is effective and safe in preventing catheter-related thrombosis is largely unknown. Our aim was to assess the incidences of catheter-related venous thrombosis and bleeding complications in children with IF receiving home parenteral nutrition (HPN) treated with primary prophylactic anticoagulation. All children, aged 0-18 years, treated with HPN at the Emma Children's Hospital/Amsterdam UMC were followed from January 2007 to July 2019. All patients were offered primary prophylactic anticoagulation from the start of HPN. The primary outcomes were catheter-related venous thrombosis and bleeding on prophylactic anticoagulation. In total, 55 (76%) of 74 patients received primary prophylactic anticoagulation. The median age at the start of prophylaxis was 8.4 (interquartile range [IQR], 5.0-55.7) months. Patients were followed for a median of 31.2 (IQR, 10.7-53.5) months, with a total of 65,463 catheter days. The incidence of catheter-related thrombosis on prophylactic anticoagulation was 0.2 per 1000 catheter days. In total, the incidence of clinically relevant bleeding was 0.1 per 1000 catheter days. The median time to first event was 1268 (IQR, 149-2014) days for thrombosis and 389 (IQR, 227-2912) days for clinically relevant bleeding. Cumulative event-free survival after 5 years was 78% for thrombosis. Our study shows a low rate of catheter-related venous thrombosis and a slightly elevated rate of clinically relevant bleeding in children receiving HPN and primary prophylactic anticoagulation.