Interpersonal space (IPS) is the area around the body that individuals maintain between themselves and others during social interactions. When others violate our IPS, feeling of discomfort rise up, urging us to move farther away and reinstate an appropriate interpersonal distance. Previous studies showed that when individuals are exposed to closeness of an unknown person (a confederate), the skin conductance response (SCR) increases. However, if the SCR is modulated according to participant's preferred IPS is still an open question. To test this hypothesis, we recorded the SCR in healthy participants when a confederate stood in front of them at various distances simulating either an approach or withdrawal movement (Experiment 1). Then, the comfort-distance task was adopted to measure IPS: participants stop the confederate, who moved either toward or away from them, when they felt comfortable with other's proximity (Experiment 2). We found higher SCR when the confederate stood closer to participants simulating an IPS intrusion, compared to when the confederate moved farther away. Crucially, we provide the first evidence that SCR, acting as a warning signal, contributes to interpersonal distance preference suggesting a functional link between behavioral components of IPS regulation and the underlying physiological processes.