- To investigate the occurrence of venous thromboembolism (VTE), clinical characteristics, risk factors, treatment outcomes, and anticoagulation safety in pediatric inflammatory bowel disease (IBD) over an 11-year period. A nested case-control study within an identified cohort was performed amongst children with IBD from 2009 to 2020 in Canada. There were 890 hospitalizations during the study period, and 15 venous thromboembolic events (1.69%) among 12 patients occurred, including 12 with ulcerative colitis and three with Crohn's disease. VTE proportions were significantly different between female (2.7%) and male (0.8%) patients (P = 0.03). VTE in the ulcerative colitis group (4.2%) was significantly higher than in the Crohn's disease group (0.6%) (P = 0.001). Central venous catheter and length of hospital stay were correlated to VTE development. Twelve of 15 (80%) with VTEs presented symptoms related to extremity thrombosis and pulmonary embolism. Nine of the 15 (60%) had a deep vein thrombosis, and 2 (13.3%) developed a severe pulmonary embolism. Seven of 15 (47%) received anticoagulation therapy for 1-6 months. VTE-related symptoms and repeat imaging tests improved with no bleeding complication in those treated with anticoagulation therapy. No patients received long-term thromboprophylaxis after antithrombotic treatment was discontinued. The VTE proportion in pediatric IBD patients was relatively low. Children with VTE were disproportionately females with ulcerative colitis compared with children without VTE. Patients with VTE had a good prognosis after anticoagulation therapy without mortality or increased bleeding events. The role of VTE screening and efficacy of thromboprophylaxis need to be further evaluated.