The ability to tune the properties of hydrogen-evolving molecular electrocatalysts is important for developing alternative energy sources. Fluorinated diglyoxime-iron complexes have been shown to evolve hydrogen at moderate overpotentials. Herein two such complexes, [(dAr(F)gBF2)2Fe(py)2], denoted A, and [(dAr(F)g2H-BF2)Fe(py)2], denoted B [dAr(F)g = bis(pentafluorophenyl-glyoximato); py = pyridine], are investigated with density functional theory calculations. B differs from A in that one BF2 bridge is replaced by a proton bridge of the form O-H-O. According to the calculations, the catalytic pathway for A involves two consecutive reduction steps, followed by protonation of an Fe(0) species to generate the active Fe(II)-hydride species. B is found to proceed via two parallel pathways, where one pathway is similar to that for A, and the additional pathway arises from protonation of the O-H-O bridge, followed by spontaneous reduction to an Fe(0) intermediate and intramolecular proton transfer from the ligand to the metal center or protonation by external acid to form the same active Fe(II)-hydride species. Simulated cyclic voltammograms (CVs) based on these mechanisms are in qualitative agreement with experimental CVs. The two parallel pathways identified for B arise from an equilibrium between the protonated and unprotonated ligand and result in two catalytic peaks in the CVs. The calculations predict that the relative probabilities for the two pathways, and therefore the relative magnitudes of the catalytic peaks, could be tuned by altering the pK(a) of the acid or the substituents on the ligands of the electrocatalyst. The ability to control the catalytic pathways through acid strength or ligand substituents is critical for designing more effective catalysts for energy conversion processes.