Background The aim of this study was to evaluate the safety and efficacy of radiofrequency ablation (RFA) for treating third degree haemorrhoids, with a follow-up over 2 years. Methods We conducted a prospective, two-centre study to assess RFA of third-degree haemorrhoids in an outpatient setting. Treatment was performed under local anaesthesia, optionally in combination with sedation. The primary endpoint was analysis of a proctological symptom score ([PSS] bleeding, itching, pain, soiling) and proctological examination to detect recurrence at 1, 6, 12 and 24 months after surgery. The secondary endpoints were postoperative complications, incidence of postoperative pain, including administration of analgesics and time to return to daily routine. Results Ninety-eight patients were included in the study. The mean age of the patients was 49.1 ± 10.9 (mean ± SD). 83 patients (84.7%) were male and 15 patients (15.3%) were female. The follow-up involved 100% (1 month), 95% (6 months), 86% (12 months) and 74% after 24 months. The individual symptom scores and overall PSS score decreased significantly in comparison to the initial score at each time point assessed. Prolapsed haemorrhoids decreased in comparison to the initial situation (100%) to 7.2% (1 month), 3.5% (6 months), 13.1% (12 months) and 13.7% (after 24 months). Thirteen patients (12.7%) required repeat haemorrhoid therapy during the 2-year follow-up period. The mean maximum pain score after the procedure was 2.5 ± 2.7 (determined with the visual analogue scale), while 33 (33.7%) patients reported having no pain. 59 (60.2%) patients did not take analgesics after the procedure. Eleven patients (11.2%) experienced minor complications (bleeding, fever, cramps, diarrhoea, anal venous thrombosis) but did not require additional treatment. Eight cases (8.2%) of major complications (infection, bleeding, severe pain) required treatment with antibiotics, a second intervention, analgesics or hospitalization. Conclusions RFA is safe and effective for treatment of third-degree haemorrhoids. The main advantages of this new method are its use on an outpatient basis under local anaesthesia, a very low level of postoperative pain and significant control of haemorrhoid symptoms over 2 years.