Molecules are promising candidates for electronic device components because of their small size, chemical tunability, and ability to self-assemble. A major challenge when building molecule-based electronic devices is forming reliable molecular junctions and controlling the electrical current through the junctions. Here, we report a three-terminal junction that combines both the ability to form a stable single-molecule junction via the mechanically controllable break junction (MCBJ) technique and the ability to shift the energy levels of the molecule by gating. Using a noncontact side-gate electrode located a few nanometers away from the molecular junction, the conductance of the molecule could be dramatically modulated because the electrical field applied to the molecular junction from the side gate changed the molecular electronic structure, as confirmed by the ab initio calculations. Our study will provide a new design for mechanically stable single-molecule transistor junctions fabricated by the MCBJ method.