We compared the changes in corneal endothelial cells and surgical outcomes after Ahmed glaucoma valve (AGV) implantation with the valve tip inserted either into ciliary sulcus (CS) or anterior chamber (AC). We retrospectively reviewed the medical records of patients treated with CS AGV (n = 24) and AC AGV (n = 38). We compared the preoperative and postoperative central corneal endothelial cell density (ECD), endothelial cell coefficient of variation (CV), best-corrected visual acuity, intraocular pressure (IOP), number of glaucoma medications, and postoperative complications in the two groups. Both groups had similar baseline characteristics and follow-up period. At the last follow-up, the AC AGV group had significantly higher mean monthly ECD loss (17.47 ± 11.50 cells/mm2 vs. 6.40 ± 7.69 cells/mm2, p < 0.0001) and greater proportion of mean monthly ECD loss than the CS AGV group (0.84 ± 0.53 vs. 0.36 ± 0.39%, p < 0.0001). Both groups had similar mean monthly CV changes. The qualified success rates at 2 years were 83.3% and 76.3% for the CS AGV and AC AGV groups, respectively. Although similar surgical outcomes including visual acuity, IOP, number of glaucoma medications, and postoperative complications were obtained following CS AGV and AC AGV, corneal ECD loss was higher in the AC AGV group. Thus, CS AGV may be a better surgical option than AC AGV.