Objective To estimate long-term recurrence, complications after percutaneous balloon compression (PBC) and radiofrequency thermocoagulation (RFT) of gasserian ganglion among a large sample of patients with trigeminal neuralgia (TN) during a long-term follow-up. Methods A retrospective analysis of 1313 patients undergoing PBC or RFT for the treatment of TN was conducted from 2006 to 2020. Recurrence-free survival (RFS) was assessed by the Kaplan-Meier method. Complications including facial numbness, corneal reflex decrease and masseter weakness were also estimated. Results For patients who received first initial PBC and RFT, the median RFS was 130.1 months (95% CI: 124.4, 135.9) and 123.3 months (95% CI: 117.6, 128.9) in PBC and RFT group with log-rank p = 0.108. The RFS rate was, respectively, 90.6% (95% CI: 88.1%-93.3%) and 91.4% (95% CI: 89.1%-93.7%) at 1 year, 84.6% (95% CI: 81.4%-87.8%) and 83.3% (95% CI: 80.3%-86.3%) at 3 years, 81.5% (95% CI: 78.1%-85.0%), and 78.6% (95% CI: 75.2%-81.9%) at 5 years, 71.5% (95% CI: 67.5%-75.5%), and 64.8% (95% CI: 61.0%-68.7%) at 10 years in two groups. No significant difference was observed in facial numbness degree between two groups after procedure. Compared with PBC group, ophthalmic complication prevalence was higher in RFT group (9.6%) (p = 0.001). However, masseter weakness incidence was lower (10.7%) than that in PBC group (24.0%) with p < 0.001. Conclusions Patients with TN seemed to attain similar long-term benefit from PBC and RFT, especially in elderly. However, in order to reduce postoperative complications, PBC provided a safer and alternative for treating TN involving ophthalmic division, whereas RFT could be employed as a preferred regimen for maxillary and mandibular TN.