Observing 3D content on a cinema or TV screen potentially generates fatigue. In psychovisual research, experience of visual symptoms following the observation of stereo-content is usually assessed thanks to questionnaires and subjective reports. We attempted to explore the occurrence of visual fatigue using more objective methods, namely by using binocular eye-tracking and psychophysics. A main objective was to study the emergence of visual fatigue in relation with eye-movement knowing the stimulation of the oculomotor system and its response. We designed an experiment in which participants were asked to perform a repeated vergence effort task, just followed by, and interlaced with, a 3D space perception task. Participants' eye movements were recorded during the whole session using an eye-tracking system. The analysis revealed that the perception of 3D shapes was gradually affected by the intensity of the vergence effort task. The effect on stereo-estimation was actually due to visual fatigue. 3D objects and scenes are perceived flatter. Results on the subjective reports of SSQ revealed that oculomotor factors were predominant in the visual symptoms. In addition, some effects and correlations on the micro-saccadic rate were obtained. This work offers a perspective to characterize objectively visual fatigue when watching stereoscopic 3D content.