According to popular models of human time perception, variations in prospective timing are caused by two factors: the pulse rate of an internal pacemaker and the amount of attention directed to the passage of time. The results concerning the effect of attention on subjective timing have been conclusive, but the mechanisms that drive the pacemaker are still far from being understood. In two experiments, we examined the impact of two factors that in the existing literature on human time perception have been argued to affect such a pacemaker: arousal and heart rate. Experienced arousal and heart rate were varied independently by means of specific physical exercises: (a) A muscle exercise increased arousal and heart rate; (b) a breath-holding exercise increased arousal but decreased heart rate; and (c) in the control condition, arousal and heart rate were held constant. The results indicate that increased subjective arousal leads to higher time estimates, whereas heart rate itself has no relevant impact on time perception. The results are discussed with respect to the underlying mechanisms of prospective time perception.