Patients with multiple sclerosis (PwMS) have a high level of fatigue and a reduced quality of life (QoL) due to the impact of multiple sclerosis (MS). Virtual reality-based therapy (VRBT) is being used to reduce disability in PwMS. The aim of this study was to assess the effect of VRBT on fatigue, the impact of MS, and QoL in PwMS. Methods: A systematic review with meta-analysis was conducted through a bibliographic search on PubMed, Scopus, Web of Science, and PEDro up to April 2021. We included randomized controlled trials (RCTs) with PwMS that received VRBT in comparison to conventional therapy (CT) including physiotherapy, balance and strength exercises, and stretching or physical activity, among others; or in comparison to simple observation; in order to assess fatigue, MS-impact, and QoL. The effect size was calculated using Cohen’s standardized mean difference with a 95% confidence interval (95% CI). Results: Twelve RCTs that provided data from 606 PwMS (42.83 ± 6.86 years old and 70% women) were included. The methodological quality mean, according to the PEDro Scale, was 5.83 ± 0.83 points. Our global findings showed that VRBT is effective at reducing fatigue (SMD −0.33; 95% CI −0.61, −0.06), lowering the impact of MS (SMD −0.3; 95% CI −0.55, −0.04), and increasing overall QoL (0.5; 95% CI 0.23, 0.76). Subgroup analysis showed the following: (1) VRBT is better than CT at reducing fatigue (SMD −0.4; 95% CI −0.7, −0.11), as well as in improving the mental dimension of QoL (SMD 0.51; 95% CI 0.02, 1); (2) VRBT is better than simple observation at reducing the impact of MS (SMD −0.61; 95% CI −0.97, −0.23) and increasing overall QoL (SMD 0.79; 95% CI 0.3, 1.28); and (3) when combined with CT, VRBT is more effective than CT in improving the global (SMD 0.6, 95% CI 0.13, 1.07), physical (SMD 0.87; 95% CI 0.3, 1.43), and mental dimensions (SMD 0.6; 95% CI 0.08, 1.11) of QoL. Conclusion: VRBT is effective at reducing fatigue and MS impact and improving QoL in PwMS.