Temporal perception abilities refer to timing mechanisms used in daily life, such as the ability to reproduce and judge time, previously associated with the basal ganglia and the cerebellum, respectively. In individuals affected by velo-cardio-facial (VCFS), both the basal ganglia and the cerebellum have been shown to be particularly vulnerable to abnormal brain development, though related temporal perception abilities have yet to be investigated. In this study, our goal was to characterize time perception and reproduction abilities in individuals with VCFS. Compared to controls, we hypothesized that individuals with VCFS would be less accurate and show more variability when reproducing a fixed-interval series of auditory beeps; furthermore, we predicted that they would show a higher perceptive acuity threshold when discriminating between subtle time differences. Forty-two subjects with VCFS and 35 matched controls participated in temporal perception evaluations. In the reproduction of time finger-tapping task, subjects were asked to press a button in cadence with a series of fixed interval beeps, and then to hold the same tempo when the beeps stopped. Overall, the VCFS group showed less accuracy and more variability in reproduction ability when compared to controls. In the second experiment, subjects were tested on auditory and visual time perception tasks. Subjects were presented with a fixed interval stimulus and a stimulus of varying duration, and were asked to determine the longer of the two. The VCFS group required a greater discrepancy between tones to accurately discriminate the two stimuli. The results point to an alteration in temporal perception associated with VCFS. Implications of altered temporal perception abilities and their relationship to the VCFS phenotype are discussed.