Using STM and AFM, we have shown that the potential created by the vanadyl-phthalocyanine molecule and the tip can trap hydrogen molecules (H2). STM topographic image showed that most of the VOPc molecules are absorbed on the herringbone kink sites of the reconstructed Au(111) surface, where they have the lowest adsorption energy. The molecules exhibit two different appearances, which can be identified as O-up and O-down with equal probability. The presence of hydrogen in the junction can be evidenced by random fluctuations of the tunneling current over time, a phenomenon called random telegraph noise. Further, the interaction with the hydrogen enables extremely high spatial resolution imaging, revealing sub-molecular features in the molecule that cannot be observed with a normal tip alone. Lastly, we evidenced that the presence of the hydrogen molecule can be directly measured by atomic force microscopy. When increasing the applied bias beyond a certain threshold the hydrogen is expelled from the junction. The insight gained in this study is expected to have wide-ranging implications from basic science to the engineering of hydrogen storage devices.