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Objectives The predominant concern during pregnancy is musculoskeletal pain, often accompanied by additional discomforts such as anxiety and insomnia. Pilates, as a low-impact mind-body exercise, may be beneficial in managing musculoskeletal pain and associated symptoms in adults. This systematic review and meta-analysis aimed to synthesise the evidence on the effectiveness of Pilates for alleviating musculoskeletal pain and other discomforts during pregnancy.Design Systematic review and meta-analysis.Data sources PubMed, Scopus, TRIP Medical Database, Web of Science and the Cochrane Central Register of Controlled Trials (CENTRAL) were searched from inception to 14 January 2026.Eligibility criteria Randomised controlled trials and prospective non-randomised controlled studies that compared Pilates with other prenatal care modalities for improving musculoskeletal pain and discomfort were eligible.Data extraction and synthesis Two researchers independently extracted data using standardised forms with subsequent cross-verification. Risk of bias was assessed using the Cochrane Risk of Bias V.2.0 tool. Meta-analyses were performed using random-effects models. The certainty of evidence was evaluated using the Grading of Recommendations Assessment, Development and Evaluation approach.Results 13 studies were included in the systematic review, of which 10 contributed data to the meta-analysis. Primary outcomes were pain intensity and disability level. Pain intensity was assessed using Visual Analogue Scale (range 0–10). Moderate-certainty evidence demonstrated that Pilates significantly reduced musculoskeletal pain during pregnancy (mean differences (MD)=−2.59, 95% CI −4.19 to −1.00; I ²=91%, p=0.001). Low-certainty evidence suggested that Pilates reduced pregnancy-related disability (standardised mean differences (SMD)=−1.82, 95% CI −2.99 to −0.66; I² = 93%, p=0.002). Secondary outcomes comprised sleep quality and psychological status. Multivariate meta-analysis showed significant improvements in psychological status (SMD=−0.86, 95% CI −1.31 to −0.42; τ²=0.4, I²=86%, p=0.0005) but did not yield statistically significant improvements in sleep quality (MD=−1.93, 95% CI −4.70 to 0.84; I²=93%, p=0.17). Both secondary outcomes were supported by very low-certainty evidence. Risk of bias assessment rated three studies as high risk, three as unclear risk and seven as low risk. Formal assessment of publication bias was not feasible owing to the limited number of studies (fewer than 10 per outcome).Conclusion This meta-analysis demonstrates that, compared with standard care, structured prenatal Pilates significantly alleviates musculoskeletal pain and disability while also enhancing psychological status.PROSPERO registration number CRD42024628027.