OBJECTIVE Evaluate the efficacy of transscleral cyclophotocoagulation versus endoscopic cyclophotocoagulation to reduce intraocular pressure. METHODS A retrospective, non-randomized cohort study with 1 year of follow-up included 62 eyes of 62 refractory glaucoma patients who underwent transscleral cyclophotocoagulation or endoscopic cyclophotocoagulation. RESULTS Thirty-two patients were enrolled in transscleral cyclophotocoagulation group and 30 patients in endoscopic cyclophotocoagulation group, and the follow-up period was 1 year. The mean preoperative intraocular pressure was 35.6 ± 12.9 mm Hg in the transscleral cyclophotocoagulation group and 31.8 ± 8.8 mm Hg in the endoscopic cyclophotocoagulation group without significant difference (p = 0.18). When we compare both groups, there was no difference at 1 month (p = 0.46) and 3 months (p = 0.21) after surgery. However, there was a statistically significant difference at month 6 (p = 0.0055) and 1 year (p = 0.0019), finding lower intraocular pressure in the transscleral cyclophotocoagulation group. Cumulative success for intraocular pressure <21 mm Hg was 93.8% in transscleral cyclophotocoagulation group and 83.3% in endoscopic cyclophotocoagulation group after 1 year (p = 0.2). For intraocular pressure <18 mm Hg, the success rate was 78.1% in transscleral cyclophotocoagulation group and 63.3% in endoscopic cyclophotocoagulation group (p = 0.06), and for intraocular pressure <16 mm Hg, the success rate was 62.5% in transscleral cyclophotocoagulation group and 43.3% in endoscopic cyclophotocoagulation group (p = 0.02). Hypotony (p = 0.01) and vision loss of two lines (p = 0.01) were statistically significant lower in endoscopic cyclophotocoagulation group. CONCLUSIONS This study demonstrates that both transscleral cyclophotocoagulation and endoscopic cyclophotocoagulation are effective at decreasing intraocular pressure. However, transscleral cyclophotocoagulation is related to more complications than endoscopic cyclophotocoagulation, whereas endoscopic cyclophotocoagulation shows lower intraocular pressure decrease than transscleral cyclophotocoagulation.