Background The coronavirus disease 2019 (COVID-19) pandemic has affected the mental health, sleep and quality of life, especially in individuals with chronic disease. Therefore, the purpose of this systematic review and meta-analysis was to investigate the impact of the COVID-19 pandemic on neuropsychiatric disorders (depression, anxiety, stress), sleep disorders (sleep quality, insomnia) and quality of life in individuals with Parkinson’s disease (PD), Multiple Sclerosis (MS) and Alzheimer's disease (AD) compared to healthy controls. Methods Seven databases (Medline, Embase, ScienceDirect, Web of Science, The Cochrane Library, Scielo and Lilacs) were searched between March 2020 and December 2022. Observational studies (i.e., cross-sectional, case–control, cohort) were included. GRADE approach was used to assess the quality of evidence and strength of the recommendation. Effect size was calculated using standardized mean differences (SMD; random effects model). A customized Downs and Black checklist was used to assess the risk of bias. Results Eighteen studies (PD = 7, MS = 11) were included. A total of 627 individuals with PD (healthy controls = 857) and 3923 individuals with MS (healthy controls = 2432) were analyzed. Twelve studies (PD = 4, MS = 8) were included in the meta-analysis. Individuals with PD had significantly elevated levels of depression (very low evidence, SMD = 0.40, p = 0.04) and stress (very low evidence, SMD = 0.60, p < 0.0001). There was no difference in anxiety (p = 0.08). Individuals with MS had significantly higher levels of depression (very low evidence, SMD = 0.73, p = 0.007) and stress (low evidence, SMD = 0.69, p = 0.03) and low quality of life (very low evidence, SMD = 0.77, p = 0.006). There was no difference in anxiety (p = 0.05) and sleep quality (p = 0.13). It was not possible to synthesize evidence in individuals with AD and sleep disorder (insomnia). Conclusion In general, the COVID-19 pandemic negatively impacted individuals with PD and MS. Individuals with PD showed significantly higher levels of depression and stress; and individuals with MS presented significantly higher depression and stress levels, as well as significantly lower quality of life when compared to healthy controls. Further studies are needed to investigate the impact of the COVID-19 pandemic in individuals with AD.