Objective This study aims to compare the efficacy and safety of AngioJet rheolytic thrombectomy vs. catheter-directed thrombolysis in patients with acute lower extremity deep vein thrombosis. Methods Between the period of February 2015 and October 2016, 65 patients with documented acute lower extremity deep vein thrombosis were treated with catheter-directed intervention. These patients were divided into two groups: AngioJet group and catheter-directed thrombolysis group. Comparisons were made with regard to efficacy and safety between these two groups. Results In the AngioJet group, complete or partial thrombus removal was accomplished in 23 (72%) and 3 (9%) patients, respectively. In the catheter-directed thrombolysis group, complete or partial thrombus removal was accomplished in 27 (82%) patients and 1 (3%) patient, respectively. In the AngioJet group, the perimeter difference between the suffered limb and healthy one declined from 5.1 ± 2.3 cm to 1.4 ± 1.2 cm ( P < 0.05). In the catheter-directed thrombolysis group, the perimeter difference declined from 4.7 ± 1.6 cm to 1.5 ± 0.9 cm ( P < 0.05). The mean urokinase dose was 0.264 ± 0.135 million units in the AngioJet group and 1.869 ± 0.528 million units in the catheter-directed thrombolysis group ( P < 0.05). The duration of thrombolysis was 4.2 ± 1.7 h in the AngioJet group and 73.6 ± 18.3 h in the catheter-directed thrombolysis group ( P < 0.05). The occurrence of complications in these two groups was 19% and 18%, respectively (not significant). Conclusion AngioJet rheolytic thrombectomy is a new, safe and effective approach for treating acute lower extremity deep vein thrombosis. When compared to catheter-directed thrombolysis, this treatment provides similar success with lower urokinase dosage and shorter duration of thrombolysis.