To evaluate the clinical outcomes and safety of radiofrequency (RF) ablation for benign non-functioning thyroid nodules over a 4-year follow-up. We evaluated 126 benign non-functioning thyroid nodules of 111 patients treated with RF ablation and followed-up more than 3 years. RF ablation was performed using the Cool-Tip RF system and an internally cooled electrode. Nodule volume and cosmetic and symptom scores were evaluated before treatment and during follow-up. Complications and factors related to efficacy were evaluated. The mean follow-up duration was 49.4 ± 13.6 months. Thyroid nodule volume decreased significantly, from 9.8 ± 8.5 ml before ablation to 0.9 ± 3.3 ml (P < 0.001) at final evaluation: a mean volume reduction of 93.4 ± 11.7 %. The mean cosmetic (P < 0.001) and symptom scores (P < 0.001) improved significantly. Factors related to efficacy were initial solidity and volume. The overall recurrence rate was 5.6 % (7/126). The overall complication rate was 3.6 % (4/111). RF ablation was effective in shrinking benign thyroid nodules and in controlling nodule-related problems over a 4-year follow-up. There were no life-threatening complications or sequelae. Therefore, RF ablation can be used as a non-surgical treatment for patients with benign non-functioning thyroid nodules.