Background: An increasing number of people suffer from chronic neck pain due to increased telecommuting. Manual therapy is considered a safe and less painful method and has been increasingly used to alleviate chronic neck pain. However, there is controversy about the effectiveness of manipulation therapy on chronic neck pain. Therefore, this systematic review and meta-analysis of randomized controlled trials (RCTs) aimed to determine the effectiveness of manipulative therapy for chronic neck pain. Methods: A search of the literature was conducted on seven databases (PubMed, Cochrane Center Register of Controlled Trials, Embase, Medline, CNKI, WanFang, and SinoMed) from the establishment of the databases to May 2022. This study included RCTs on chronic neck pain managed with manipulative therapy compared with sham, exercise, and other physical therapies. The retrieved records were independently reviewed by two researchers. Further, the methodological quality was evaluated using the PEDro scale. All statistical analyses were performed using RevMan V.5.3 software. The Grading of Recommendations, Assessment, Development and Evaluations (GRADE) assessment was used to evaluate the quality of the study results. Results: Seventeen RCTs, including 1190 participants, were included in this meta-analysis. Manipulative therapy showed better results regarding pain intensity and neck disability than the control group. Manipulative therapy was shown to relieve pain intensity (SMD = -0.83; 95% confidence interval [CI] = [-1.04 to -0.62]; p < 0.0001) and neck disability (MD = -3.65; 95% CI = [-5.67 to - 1.62]; p = 0.004). However, the studies had high heterogeneity, which could be explained by the type and control interventions. In addition, there were no significant differences in adverse events between the intervention and the control groups. Conclusions: Manipulative therapy reduces the degree of chronic neck pain and neck disabilities.