Binocular disparity provides one of the important depth cues within stereoscopic three‐dimensional (3D) visualization technology. However, there is limited research on its effect on learning within a 3D augmented reality (AR) environment. This study evaluated the effect of binocular disparity on the acquisition of anatomical knowledge and perceived cognitive load in relation to visual‐spatial abilities. In a double‐center randomized controlled trial, first‐year (bio)medical undergraduates studied lower extremity anatomy in an interactive 3D AR environment either with a stereoscopic 3D view (n = 32) or monoscopic 3D view (n = 34). Visual‐spatial abilities were tested with a mental rotation test. Anatomical knowledge was assessed by a validated 30‐item written test and 30‐item specimen test. Cognitive load was measured by the NASA‐TLX questionnaire. Students in the stereoscopic 3D and monoscopic 3D groups performed equally well in terms of percentage correct answers (written test: 47.9 ± 15.8 vs. 49.1 ± 18.3; P = 0.635; specimen test: 43.0 ± 17.9 vs. 46.3 ± 15.1; P = 0.429), and perceived cognitive load scores (6.2 ± 1.0 vs. 6.2 ± 1.3; P = 0.992). Regardless of intervention, visual‐spatial abilities were positively associated with the specimen test scores (η2 = 0.13, P = 0.003), perceived representativeness of the anatomy test questions (P = 0.010) and subjective improvement in anatomy knowledge (P < 0.001). In conclusion, binocular disparity does not improve learning anatomy. Motion parallax should be considered as another important depth cue that contributes to depth perception during learning in a stereoscopic 3D AR environment.