We modulate the conductance of electrochemically inactive molecules in single-molecule junctions using an electrolytic gate to controllably tune the energy level alignment of the system. Molecular junctions that conduct through their highest occupied molecular orbital show a decrease in conductance when applying a positive electrochemical potential, and those that conduct though their lowest unoccupied molecular orbital show the opposite trend. We fit the experimentally measured conductance data as a function of gate voltage with a Lorentzian function and find the fitting parameters to be in quantitative agreement with self-energy corrected density functional theory calculations of transmission probability across single-molecule junctions. This work shows that electrochemical gating can directly modulate the alignment of the conducting orbital relative to the metal Fermi energy, thereby changing the junction transport properties.