The purpose of this study was to analyse the changes in flare values after Micropulse Transscleral Laser Treatment for Glaucoma (MP-TLT) in patients with refractory glaucoma and to compare with the outcomes of patients who underwent continuous wave (CW) diode laser cyclophotocoagulation (CW-TSCPC). In this single-centre study, we reviewed the medical records of 54 patients who underwent MP-TLT and 35 patients who underwent CW-TSCPC at Ankara University Faculty of Medicine, Department of Ophthalmology. Aqueous flare values were measured by laser flare photometry. The mean laser flare values in both groups (MP-TLT/CW-TSCPC) increased after surgery from 20.85 ± 8.74/22.14 ± 7.39 ph/ms at baseline to 48.52 ± 18.23/57.38 ± 20.08 ph/ms (P = .001) on day 1 and then progressively decreased to 44.13 ± 18.32/52.24 ± 20.56 in week 1, 40.5 ± 18.5/48.24 ± 19.23 week 2 and 35.28 ± 17.09/41.11 ± 16.7 month 1 (all p < .05) and returned to similar levels to baseline at month 3 and month 6 (both p > .05). Patients who achieved treatment success had significantly higher flare values than patients who failed on post-operative day 1, week 1 and week 2 in both groups. The flare values were significantly lower in the MP-TLT group than the CW-TSCPC group on post-operative day 1, week 1, week 2 and month 1 (all p < .05). There were no cases of prolonged post-operative inflammation or serious complications in both groups. Intraocular inflammation, quantified by aqueous flare, may be a contributing factor to the IOP lowering effect of transscleral diode laser cyclophotocoagulation in the early post-operative period.