•Paced respiration increases PSNS activity.•Increased PSNS activity shortens perceived duration.•PSNS activity can distort time perception independently of SNS activity. Theories of human temporal perception suggest that changes in physiological arousal distort the perceived duration of events. Behavioural manipulations of sympathetic nervous system (SNS) activity support this suggestion, however the effects of behavioural manipulations of parasympathetic (PSNS) activity on time perception are unclear. The current study examined the effect of a paced respiration exercise known to increase PSNS activity on sub-second duration estimates. Participants estimated the duration of negatively and neutrally valenced images following a period of normal and paced breathing. PSNS and SNS activity were indexed by high-frequency heart-rate variability and pre-ejection period respectively. Paced breathing increased PSNS activity and reduced the perceived duration of the negative and neutrally valenced stimuli relative to normal breathing. The results show that manipulations of PSNS activity can distort time in the absence of a change in SNS activity. They also suggest that activities which increase PSNS activity may be effective in reducing the perceived duration of short events.