In a context in which virtual reality making use of S3D is ubiquitous in certain industries, as well as the substantial amount of literature about the visual fatigue S3D causes, we wondered whether the presentation of intermittent S3D stimuli would lead to improved depth perception (over monoscopic) while reducing subjects’ visual asthenopia. In a between-subjects design, 60 individuals under 40 years old were tested in four different conditions, with head-tracking enabled: two intermittent S3D conditions (Stereo @ beginning, Stereo @ end) and two control conditions (Mono, Stereo). Several optometric variables were measured pre- and post-experiment, and a subjective questionnaire assessing discomfort was administered. Our results suggest a difference between simple scenes (containing few static objects, or slow, linear movement along one axis only), and more complex environments with more diverse movement. In the former case, Stereo @ beginning leads to depth perception which is as accurate as Stereo, and any condition involving S3D leads to more precision than Mono. We posit that the brain might build an initial depth map of the environment, which it keeps using after the suppression of disparity cues. In the case of more complex scenes, Stereo @ end leads to more accurate decisions: the brain might possibly need additional depth cues to reach an accurate decision. Stereo and Stereo @ beginning also significantly decrease response times, suggesting that the presence of disparity cues at task onset boosts the brain’s confidence in its initial evaluation of the environment’s depth map. Our results concerning fatigue, while not definitive, hint at it being proportional to the amount of exposure to S3D stimuli.