The ability to perceive differences in depth is important in many daily life situations. It is also of relevance in laparoscopic surgical procedures that require the extrapolation of three-dimensional visual information from two-dimensional planar images. Besides visual-motor coordination, laparoscopic skills and binocular depth perception are demanding visual tasks for which learning is important. This study explored potential relations between binocular depth perception and individual variations in performance gains during laparoscopic skill acquisition in medical students naïve of such procedures. Individual differences in perceptual learning of binocular depth discrimination when performing a random dot stereogram (RDS) task were measured as variations in the slope changes of the logistic disparity psychometric curves from the first to the last blocks of the experiment. The results showed that not only did the individuals differ in their depth discrimination; the extent with which this performance changed across blocks also differed substantially between individuals. Of note, individual differences in perceptual learning of depth discrimination are associated with performance gains from laparoscopic skill training, both with respect to movement speed and an efficiency score that considered both speed and precision. These results indicate that learning-related benefits for enhancing demanding visual processes are, in part, shared between these two tasks. Future studies that include a broader selection of task-varying monocular and binocular cues as well as visual-motor coordination are needed to further investigate potential mechanistic relations between depth perceptual learning and laparoscopic skill acquisition. A deeper understanding of these mechanisms would be important for applied research that aims at designing behavioral interventions for enhancing technology-assisted laparoscopic skills.