Pediatric cerebral venous sinus thrombosis (CVST) is a rare complication of ulcerative colitis. Ulcerative colitis is a form of inflammatory bowel disease which accentuates hypercoagulation, thereby leading to thrombosis. Herein, we report a case of a 10-year-old girl who presented with chief complaints of headache, confusion, and new-onset seizure activity for one month as progressively worsening sequelae of ulcerative colitis. Her magnetic resonance venogram confirmed thrombosis in the right transverse, sigmoid, and superior sagittal sinus. The acute ulcerative colitis flare was managed with a short course of steroids and anti-inflammatory monoclonal antibody, and CVST got improved with low-molecular-weight heparin (LMWH). Our study emphasizes the emergence of fatal complications of ulcerative colitis in the pediatric population. It also endorses the pivotal role of thromboprophylaxis with LMWH in pediatric CVST patients. Nevertheless, further studies are required to standardize the use of LMWH in clinical practice.