Background Endovenous thermal ablation for chronic venous disease treatment is recommended over traditional surgery. The present investigation compares endovenous laser ablation (EVLA) with radiofrequency (RF) for segmental endovenous sapheno–femoral junction ablation. Methods This is a retrospective study in which 79 patients underwent a 6 cm great saphenous vein ablation by RF or by EVLA. Primary outcome was occlusion rate. Secondary outcomes included Venous Clinical Severity Score (VCSS), Aberdeen Varicose Vein Questionnaire (AVVQ) score, peri-procedural pain, aesthetic satisfaction. Results At 12 ± 1 months recanalization of shrunk tract was recorded in 5/85 (5.8%) cases (2 RF, 3 EVLA) [OR: 1.6; 95%CI: 0.2–10.4; P = 0.6689]. Two cases (1/44 RF group and 1/38 EVLA group) also showed reflux recurrence [OR: 1.0; 95%CI: 0.06–17.8; P = 1.0000]. No significant differences between groups were found in AVVQ, VCSS, peri-procedural pain, or aesthetic satisfaction. Conclusion Saphenous sparing is feasible and effective by means of both EVLA and RF, representing a possible alternative to surgery.