To evaluate for increased rectal bleeding following enoxaparin thromboprophylaxis in children hospitalized for ulcerative colitis (UC). Retrospective cohort study (2007--2016) of 218 inpatients with active UC. Patients receiving enoxaparin were compared with a nonenoxaparin-treated patient group. Severity of UC was determined using the Pediatric Ulcerative Colitis Activity Index (PUCAI). Hemoglobin (Hb) values and packed red blood cell (pRBC) transfusions were reviewed for a 7-day period following hospital admission. A linear mixed effect model was used to compare change in Hb values between the groups. Risk of pRBC transfusion was compared using a log-rank test and Cox proportional hazard regression. A sub-analysis was also conducted restricting to patients with severe UC to provide more generalizable insight into safety profile of enoxaparin. Children hospitalized for UC and receiving enoxaparin were more likely to have severe disease, received infliximab therapy and be admitted after 2010. Use of enoxaparin showed there was not a difference (P = 0.60) in the fall of Hb detected among those with acute severe colitis (initial PUCAI ≥65) during the week following admission. Moreover, there was no difference in the risk of requiring a pRBC transfusion with enoxaparin use (log-rank test all patients: P = 0.80; severe UC: P = 0.88; Cox proportional hazard regression all patients: P = 0.72; severe UC: 0.85). There was no difference in Hb levels or need for blood transfusions in children hospitalized for severe UC (PUCAI ≥65) whether or not they received enoxaparin for thromboembolism prophylaxis.