Time perception, crucial for adaptive behavior, has been shown to be altered by emotion. An arousal-dependent mechanism is proposed to account for such an effect. Yet, physiological measure of arousal related with emotional timing is still lacking. We addressed this question using skin conductance response (SCR) in an emotion regulation paradigm. Nineteen participants estimated durations of neutral and negative sounds by comparing them to a previously memorized duration. Instructions were given to attend either to temporal or to emotional stimulus features. Attending to emotion with negative sounds generated longer subjective duration and greater physiological arousal than attending to time. However, a shared-attention condition showed discrepancy between behavioral and physiological results. Supporting the idea of a link between autonomic arousal and subjective duration, our results however suggest that this relation is not as direct as was expected. Results are discussed within recent model linking time perception, emotion and awareness.