Ion transport processes through protein channels is an essential component of cellular function. One especially interesting example is the ClC-ec1 antiporter, which transports proton (H+) and chloride ions (Cl-) in opposite directions with a stoichiometric ratio of 1:2. In this work, the multistate empirical valence bond (MS-EVB) molecular dynamics method has been applied to simulate the explicit translocation of a Grotthuss shuttling excess proton from the intracellular residue Glu203 to the extracellular residue Glu148 through a transient water chain inside the channel. The minimum energy proton transport pathway was first identified using the string method and the free energy profile, i.e., the potential of mean force (PMF), was calculated along the path. The electrostatic coupling between the excess proton and chloride ion was also explored. These studies therefore provide a more detailed picture of the proton transport process in the ClC-ecl antiporter.