Vascular thromboses are a significant cause of morbidity and mortality in children. Data in children regarding catheter-based rheolytic and aspiration thrombectomy systems are limited. We sought to review the safety and efficacy of catheter-based rheolytic and aspiration thrombectomy systems in children. Methods: Data of all children having undergone thrombectomy using specialized rheolytic or aspiration systems were reviewed. Results: Thrombectomy was performed in 50 vessels in 21 patients, median age 1.9 months (8 days–18 yrs), median weight 4.3 (1.1–67.9) kg. Thrombectomy was performed using AngioJet in 16, Helix Clot Buster in 5, Fetch catheter in 8, Pronto catheter in 1, and a combination of other systems in 20 vessels (with AngioJet in 16). Thrombectomy was successful in 47/50 (94%) vessels in 18/21 (86%) patients with additional balloon/stent therapy or tPA administration performed in 16/18 (89%) of these patients. There were 2 (9.5%) major complications (both with AngioJet) consisting of asystole when thrombectomy was performed using activation times of >5 sec. At a median follow-up of 10 months (2 weeks–7 years), all 47 successfully treated vessels are patent, with 8/18 (44%) patients requiring reintervention with angioplasty/stent placement or repeat thrombectomy. Conclusions: Catheter-based thrombectomy systems are an important adjunctive tool in the treatment of children with thrombotic vessel occlusions. Significant hemodynamic compromise seen when using AngioJet may be minimized by using activation times of ≤5 sec. © 2016 Wiley Periodicals, Inc.