Background: The aim of this study was to compare the safety and efficacy of primary trabeculectomy with mitomycin C and Ahmed glaucoma valve (AGV) implantation in patients with Fuchs heterochromic iridocyclitis (FHIC)-related glaucoma, a rare complication of an uncommon form of uveitis. Methods: In this retrospective comparative case series, 26 FHIC-associated glaucoma patients received trabeculectomy (n=12) or an AGV (n=14). Primary outcome measures were surgical success, defined as intraocular pressure (IOP) ≤21 mmHg, decreasing ≥20% from baseline, and no secondary glaucoma surgery. Secondary outcome measures were the number of glaucoma medications, complications, best corrected visual acuity (BCVA), and IOP. Results: The follow-up was 34.0±17.7 months in patients that received trabeculectomy and 33.4±18.6 months in AGV (P= 0.837). The cumulative probability of success rate was 41.7% for trabeculectomy and 85.7% for AGV, with no significant difference in complications (P>0.05). The IOP in patients that received trabeculectomy dropped from 23.4±3.3 mmHg to 21.6±5.2 mmHg at the final visit (P= 0.041). In patients that received AGV, the IOP decreased from 24±7.8 to 17.1±2.6 mmHg (P= 0.003). The number of glaucoma medications at baseline were 3.3±0.5 in those that received trabeculectomy and 3±0.6 in those that received AGV (P=0.233), and decreased to 2.4±1.0 (P=0.008) and 1.7±0.6 (P=0.002), respectively. BCVA was equal in both groups and did not change (P>0.05). Conclusion: Primary AGV had a higher success rate than trabeculectomy, with patients also needing fewer medications for the management of FHIC-associated glaucoma.