Emotional distortions of the perceived duration of events are often explained in terms of increases and decreases in arousal. While this explanation is theoretically plausible, there is a lack of evidence for a direct relationship between physiological arousal and perceived duration. The aim of the current study was to investigate whether physiological arousal, defined by autonomic nervous system (ANS) activity is directly related to perceived duration. In two experiments we measured skin conductance level (SCL) and high frequency heart rate variability (HF HRV) during verbal estimation tasks. In Experiment 1, participants estimated the duration of electro-cutaneous stimuli previously rated as inducing no pain, low pain and high pain. High intensity stimuli were perceived as lasting for longer than low intensity stimuli, and these changes in duration estimation were associated with changes in ANS activity. In Experiment 2, participants estimated the duration of a neutral visual stimulus while experiencing different intensities of background thermal pain (no pain, low pain, and high pain), to determine whether task-irrelevant arousal also affects time perception. Duration estimations for the neutral stimulus did not increase with pain intensity despite significant increases in SCL. Furthermore, there was no association between ANS activity and time estimation in Experiment 2. These findings suggest that the relationship between physiological arousal and time perception is more complex than previously described. While physiological arousal can influence the perceived duration of events, it appears to have a greater capacity to do so when the to-be-timed stimulus is itself the source of arousal. (PsycINFO Database Record (c) 2019 APA, all rights reserved).