A case of an adult with anisometropic amblyopia who underwent a successful vision therapy program playing videogames in a virtual reality environment is described, reporting changes in conventional visual clinical data, as well as in brain activity. The patient was a 22 year old man on baseline examination that never previously wore correction for his anisometropia. After prescribing contact lens correction for the anisometropia and after 44 h of virtual reality-based vision therapy over a period of 1.5 years, the best corrected distance visual acuity (BCDVA) in the amblyopic eye improved from 0.05 to 0.5 (Sloan chart). One year after finishing the visual training, the BCDVA experienced a slight decrease to 0.4 (Sloan chart). Through the visual training, the patient gradually developed stereopsis. Likewise, changes were also detected after visual therapy on functional magnetic resonance imaging while the patient was viewing 2D and 3D stimuli. The preliminary results of this case show the potential of using virtual reality-based visual training as a treatment for adult amblyopia.