Catheter-related thrombosis (CRT) is a devastating complication of central venous catheters in children with intestinal failure (IF), but the optimal preventive therapy of CRT is unknown. This study assessed the efficacy and safety of 2 protocols of secondary anticoagulation prophylaxis with low-molecular-weight heparin (LMWH). This is a comparative cohort study of children from 2 IF programs who received secondary anticoagulation prophylaxis with LMWH for CRT. The short-term protocol group (N = 13) received therapeutic dosing until thrombus resolution or ≤3 months. In the long-term protocol group (N = 26), prophylactic dosing continued until line removal. Patients underwent routine annual vascular ultrasound and were followed for ≥1 year. The primary outcome was development of secondary thrombosis; post hoc analysis assessed rates of secondary thrombosis at 12 months. Patient demographics were similar between groups. Secondary thrombosis occurred in 8 of 13 (62%) patients in the short-term group and in 9 of 26 (35%) in the long-term protocol group (P = .019) in a median time of 144.5 and 689 days, respectively (P = .01). Secondary thrombosis within 12 months occurred in 7 of 13 (54%, short term) and 2 of 26 (8%, long term) patients (P = .001). Secondary thrombosis was associated with catheter replacements (23.5 vs 5.5 catheters per 1000 catheter days; P = .016) and longer daily parenteral nutrition (PN) infusion (24 vs 15.25 hours; P = .044). Compliance was good (>80% of doses) in 92% of patients. Long-term secondary anticoagulation prophylaxis with LMWH reduces the incidence of secondary thrombosis and should be considered in children with CRT that require PN for prolonged periods of time.