Stroke represents a major health challenge worldwide, often resulting in significant long-term disability that affects cognitive, motor, and emotional functions. Rehabilitation strategies that enhance patient motivation are crucial for improving outcomes. This randomized controlled trial investigated the impact of Virtual Reality Rehabilitation Systems (VRRS) compared to traditional cognitive training on motivation, cognitive recovery, and emotional state in post-stroke patients. Fifty-four adults with chronic stroke were randomized into two equal groups (27 participants per group). The experimental group received 24 sessions of Virtual Reality (VR) cognitive training, while the control group underwent 24 sessions of traditional cognitive rehabilitation. Motivation was assessed using the McClelland test, while cognitive and emotional states were evaluated using the Montreal Cognitive Assessment (MoCA) and Hamilton Rating Scales for Anxiety and Depression (HAM-A, HAM-D). The experimental group exhibited significant improvements in motivation, with marked increases in Achievement (T0: 68.41 ± 15.81, T1: 68.93 ± 15.80; p < 0.001) and Affiliation(T0: 60.67 ± 14.64, T1: 60.93 ± 15.59; p = 0.006) dimensions, alongside enhanced cognitive function (T0: 24.781 ± 1.89, T1: 26 (24.5-27); p = 0.001), reduced depressive (T0: 41 ± 2.32, T1: 6 (4-8); p = 0.003) and anxiety symptoms (T0: 4.26 ± 1.99, T1: 3.30 ± 1.94; p < 0.001). The Control Group showed significant differences only in MOCA (T0: 25 (23-26.5), T1: 25 (24-27); p < 0.001). Between-group analysis revealed no significant differences between the two groups. These findings underscore the potential of VR as a multifaceted tool to boost motivation, facilitate cognitive recovery, and improve emotional state, offering a comprehensive approach to post-stroke rehabilitation.