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Proton transfer plays a crucial role in various chemical and biological processes. A major theoretical challenge in simulating proton transfer arises from the quantum nature of the proton. The constrained nuclear-electronic orbital (CNEO) framework was recently developed to efficiently and accurately account for nuclear quantum effects, particularly quantum nuclear delocalization effects, in quantum chemistry calculations and molecular dynamics simulations. In this paper, we systematically investigate challenging proton transfer modes in a series of shared-proton systems using CNEO density functional theory (CNEO-DFT), focusing on evaluating existing electron–proton correlation functionals. Our results show that CNEO-DFT accurately describes proton transfer vibrational modes and significantly outperforms conventional DFT. The inclusion of the epc17-2 electron–proton correlation functional in CNEO-DFT produces similar performance to that without electron–proton correlations, while the epc17-1 functional yields less accurate results, comparable with conventional DFT. These findings hold true for both asymmetrical and symmetrical shared-proton systems. Therefore, until a more accurate electron–proton correlation functional is developed, we currently recommend performing vibrational spectrum calculations using CNEO-DFT without electron–proton correlation functionals.