Purpose: To compare the clinical outcomes of penetrating keratoplasty (PKP) and Descemet stripping automated endothelial keratoplasty (DSAEK) in eyes with Glaucoma Ahmed Valve implants. Methods: The charts of 11 patients who underwent PKP and 11 who underwent DSAEK between February 2016 and June 2018 were retrospectively reviewed; all patients previously underwent Ahmed valve implant surgery. The best corrected visual acuity, intraocular pressure, and endothelial cell count were compared 1, 3, and 6 months after surgery. Graft rejection and graft failure were also evaluated during follow-up. The survival rates were compared using Kaplan–Meier survival analysis. Results: The difference in graft survival rates of the PKP and DSAEK groups was not significant (p = 0.295); however, graft failure occurred earlier in the PKP group (12.9 ± 10.1 vs. 18.8 ± 5.3 months). The postoperative best corrected visual acuity of the PKP group had improved at 1 (p = 0.027) and 3 (p = 0.017) months, while the DSAEK group showed significant improvement at 1, 3, and 6 months (all p = 0.005). Intergroup analysis showed better visual prognosis of the DSAEK group at 1, 3, and 6 months after surgery (p = 0.023, p = 0.007, and p = 0.004, respectively). Conclusions In our study, the two corneal transplantation methods did not have significantly different graft survival rates; however, graft failure occured later in the DSAEK group and the postoperative visual acuity was better than in the PKP group. Although further study is needed, performing DSAEK in patients with an Ahmed valve implant seems to be a good alternative to PKP.