Many problems such as delamination, cracking, fiber tearing, ovality, and surface roughness are encountered in the drilling of glass-fiber-reinforced composite (GFRP) materials. In this study, the percentage of multi-walled carbon nano tube (MWCNT), cutting tool type, feed rate, and cutting speed were selected as control factors during the drilling of MWCNT-reinforced GFRP nanocomposites. The quality characteristics of the drilling process were determined as surface roughness, delamination, torque, and thrust force. The experiments were carried out in accordance with the Taguchi L27 orthogonal array. The lowest values obtained because of the experiments were Ra = 4.95 µm, Dm = 1.099, T = 14.78 N, and F = 44.24 N, respectively. However, since each of these outputs were obtained from different experimental trials, different multi-criteria decision-making (MCDM) methods were used to optimize all outputs at the same time. First, the criteria were weighted using the fuzzy AHP method, and then the outputs were optimized using multi-criteria decision-making methods (i.e., GRA, WASPAS and VIKOR). Very close optimal ranking was obtained in all three methods. The best results were obtained for Ra = 4.86 µm, Dm = 1.13, T = 55.57 N, and F = 48.00 N. In the next step, the performance values obtained from each MCDM method were re-optimized using the Taguchi S/N ratio method. By comparing between these models, a single optimal condition for drilling is proposed. Accordingly, A2B3C1D1 (Ra = 4.86 µm, Dm = 1.10, T = 17.47 N and F = 48.33 N) for FAHP-GRA and FAHP-WASPAS and A2B3C2D2 (Ra = 5.02 µm, Dm = 1.09, T = 37.19 N and F = 45.01 N) for FAHP-VIKOR were determined as the best performing experiments. Finally, validation tests were conducted to compare the performance of the experiments. As a result, the FAHP-GRA and FAHP-WASPAS optimization with Taguchi S/N gave an unweighted improvement of 82.9% and a weighted improvement of 10.04% compared to the results of the experiment with MCDM. Compared to the results of the experiments with MCDM, S/N FAHP-VIKOR provided an unweighted improvement of 52.75% and a weighted improvement of 8.19%. According to the results obtained, for this study, FAHP-GRA and FAHP-WASPAS are more effective optimization methods than FAHP-VIKOR.