BACKGROUND Microvascular decompression (MVD) is a well accepted surgical treatment strategy for trigeminal neuralgia (TN) with satisfying long-term outcome. However, considerable recurrent patients need more effective management. The purpose of this study was to evaluate the effectiveness of radiofrequency thermocoagulation rhizotomy (RTR) on patients with recurrent TN after MVD. METHODS Totally 62 cases of recurrent TN after MVD undergoing RTR from January 2000 to January 2010 were retrospectively evaluated. Based on surgical procedures undertaken, these 62 cases were classified into two subgroups: group A consisted of 23 cases that underwent traditional RTR by free-hand; group B consisted of 39 cases that underwent RTR under the guidance of virtual reality imaging technique or neuronavigation system. The patients in group A were followed up for 14 to 70 months (mean, 40 ± 4), and those in group B were followed up for 13 to 65 months (mean, 46 ± 7). Kaplan-Meier analyses of the pain-free survival curves were used for the censored survival data, and the log-rank test was used to compare survival curves of the two groups. RESULTS All patients in both groups A and B attained immediate pain relief after RTR. Both groups attained good pain relief rate within the first two years of follow-up: 92.3%, 84.6% and 82.6%, 69.6% respectively (P > 0.05). After 2 years, the virtual reality or neuronavigation assisted RTR group (group B) demonstrated higher pain relief rates of 82.5%, 76.2% and 68.8% at 3, 4 and 5 years after operation respectively, while those in group A was 57.2%, 49.6%, and 36.4% (P < 0.05). Low levels of minor complications were recorded, while neither mortalities nor significant morbidity was documented. CONCLUSIONS RTR was effective in alleviating the pain of TN cases suffering from unsuccessful MVD management. With the help of virtual reality imaging technique or neuronavigation system, the patients could attain better long-term pain relief.