Psychology and neuroscience research have shown that fractioning operations among several individuals along a hierarchical chain allows diffusing responsibility between components of the chain, which has the potential to disinhibit antisocial actions. Here, we present two studies, one using fMRI (Study 1) and one using EEG (Study 2), designed to help understand how commanding or being in an intermediary position impacts the sense of agency and empathy for pain. In the age of military drones, we also explored whether commanding a human or robot agent influences these measures. This was done within a single behavioral paradigm in which participants could freely decide whether or not to send painful shocks to another participant in exchange for money. In Study 1, fMRI reveals that activation in social cognition-related and empathy-related brain regions was equally low when witnessing a victim receive a painful shock while participants were either commander or simple intermediary transmitting an order, compared with being the agent directly delivering the shock. In Study 2, results indicated that the sense of agency did not differ between commanders and intermediary, no matter whether the executing agent was a robot or a human. However, we observed that the neural response over P3 event-related potential was higher when the executing agent was a robot compared with a human. Source reconstruction of the EEG signal revealed that this effect was mediated by areas including the insula and ACC. Results are discussed regarding the interplay between the sense of agency and empathy for pain for decision-making.