Objective We evaluated our experience with segmental radiofrequency ablation (RFA) of the small saphenous vein (SSV), a less common procedure than great saphenous vein ablation, and developed a classification system and algorithm for endovenous heat-induced thrombus (EHIT), based on modifications of our prior algorithm of EHIT following great saphenous ablation. Methods Endovenous ablation was performed on symptomatic patients with incompetent SSVs following a minimum of 3 months of compression therapy. Demographic data, risk factors, CEAP classification, procedure details, and follow-up data were recorded. A four-tier classification system and treatment algorithm was developed, based on EHIT proximity to the popliteal vein. Results Eighty limbs (in 76 patients) were treated with RFA of the SSV between January 2008 and August 2012. Duplex ultrasound was performed between 24 and 72 hours postprocedure in all patients. Ablation was successful in 98.7% (79/80) of procedures. Sixty-eight (85%) patients had level A closures (≥1 mm caudal to popliteal vein) and 10 patients (13%) had level B closures (flush with popliteal vein) and were observed. Two limbs (3%) had EHIT extending into the popliteal vein (level C) and were treated with outpatient low-molecular-weight heparin anticoagulation. Thrombus retracted to the level of the saphenopopliteal junction in both patients following a short course of anticoagulation. No patient developed an occlusive deep vein thrombosis (DVT) (level D). Mean follow-up period was 6.2 months; no patient had small saphenous recanalization, occlusive DVT, or pulmonary embolus. The presence or absence of the Giacomini vein was not predictive of level B and C closure. Conclusions RFA of the SSV in symptomatic patients has a high success rate with a low risk of DVT. A classification system and treatment protocol based on the level of EHIT in relation to the saphenopopliteal junction is useful in managing patients. The approach to patients with thrombus flush with the popliteal vein or bulging has not been previously defined; our outcomes were excellent, using our treatment algorithm.