Objectives F-care (endovenous radiofrequency, F Care Systems, Antwerp, Belgium) is a relatively new radiofrequency ablation technique for the treatment of venous insufficiency. There is a lack of published data about F-care in literature. This study aimed to prospectively compare the F-care method with conventional endovenous radiofrequency ablation Closurefast method for the management of incompetent great saphenous veins. Methods Between June 2015 and December 2018, 114 patients with incompetent varicose veins were treated either with the F-care or Closurefast. The pre-, intra-, postprocedural, and follow-up data of the patients were collected and prospectively compared. Results The average ablated vein length was 23.1 ± 4 cm in the F-care group and 26.6 ± 4 cm in the Closurefast group ( P = 0.01). The average procedure time was 17.4 ± 4 min (range: 10–30 min) in the F-care group, and 17.1 ± 3 min (range: 11–27 min) in the Closurefast group ( P = 0.77). The one-month total occlusion rates in the F-care and Closurefast groups were 96.2% and 98.1%, respectively ( P = 0.5). The one-year full occlusion rates in the F-care and Closurefast groups were 71.7% and 90.6%, respectively ( P = 0.013). In both the F-care and Closurefast groups, the venous clinical severity scores declined significantly with no difference between groups. There was no significant difference between adverse events following F-care treatment compared with Closurefast treatment ( P ≤ 0.05). Conclusions The F-care system was as safe and fast, but the one-year closure rate was significantly lower when compared to the other method. There was no significant difference between the adverse effects of both approaches. Further large-scale, multi-center prospective studies with long-term outcomes are required to identify the effectiveness of F-care treatment modality for patients with saphenous vein insufficiency.