Time experience is an essential part of one’s perception of any environment, real or virtual. In this article, from a virtual environment design perspective, we explore how rhythmic stimuli can influence an unrelated cognitive task regarding time experience and performance in virtual reality. This study explicitly includes physiological data to investigate how, overall, experience correlates with psychophysiological observations. The task involves sorting 3D objects by shape, with varying rhythmic stimuli in terms of their tempo and sensory channel (auditory and/or visual) in different trials, to collect subjective measures of time estimation and judgment. The results indicate different effects on time experience and performance depending on the context, such as user fatigue and trial repetition. Depending on the context, a positive impact of audio stimuli or a negative impact of visual stimuli on task performance can be observed, as well as time being underestimated concerning tempo in relation to task familiarity. However, some effects are consistent regardless of context, such as time being judged to pass faster with additional stimuli or consistent correlations between participants’ performance and time experience, suggesting flow-related aspects. We also observe correlations between time experience with eye-tracking data and body temperature, yet some of these correlations may be due to a confounding effect of fatigue. If confirmed as separate from fatigue, these physiological data could be used as reference point for evaluating a user’s time experience. This might be of great interest for designing virtual environments, as purposeful stimuli can strongly influence task performance and time experience, both essential components of virtual environment user experience.