BackgroundRobust routine immunization schedules for pertussis-containing vaccines have been applied for years, but pertussis outbreaks remain a worldwide problem. This study aimed to investigate the association between vaccine hesitancy and pertussis in infants and children.MethodsWe searched PubMed, Cochrane, Web of Science, Embase, and China National Knowledge Internet for studies published between January 2012 and June 2022. This study included case–control and cohort studies that assessed the association between childhood/maternal vaccine hesitancy and odds ratios (ORs), risk ratios (RRs), and vaccine effectiveness (VE) related to pertussis in infants and children\documentclass[12pt]{minimal}
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				\begin{document}$$\le$$\end{document}≤9 years old. ORs/VEs with a 95% confidence interval (CI) were calculated. Random-effects meta-analysis models were used for appropriate pooled estimates, and heterogeneity was assessed using\documentclass[12pt]{minimal}
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				\begin{document}$${I}^{2}$$\end{document}I2. Cumulative meta-analysis and subgroup analyses stratified by study characteristics were performed.ResultsTwenty-two studies were included, with a mean quality score of 7.0 (range 6.0–9.0). Infants and children with pertussis were associated with higher vaccine hesitancy to all doses (OR = 4.12 [95% CI: 3.09–5.50]). The highest OR was between children who were unvaccinated over four doses and children who were fully vaccinated (OR = 14.26 [95%CI: 7.62–26.70]); childhood vaccine delay was not statistically significantly associated with pertussis risk (OR = 1.18 [95% CI: 0.74–1.89]). Maternal vaccine hesitancy was associated with significantly higher pertussis risk in infants aged 2 and 3 months old, with higher pertussis ORs in infants\documentclass[12pt]{minimal}
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				\begin{document}$$\le$$\end{document}≤2 months old (OR = 6.02 [95%CI: 4.31–8.50], OR = 5.14 [95%CI: 1.95–13.52] for infants\documentclass[12pt]{minimal}
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				\begin{document}$$\le$$\end{document}≤2 and\documentclass[12pt]{minimal}
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				\begin{document}$$\le$$\end{document}≤3 months old, respectively). Maternal and childhood VEs were high in reducing pertussis infection in infants and children. The administration time of maternal vaccination had little effect on VE.ConclusionVaccine hesitancy increased pertussis risks in infants and children. Ensuring that children receive up-to-date pertussis vaccines is essential; short delays in receiving childhood vaccinations may be unimportant. Maternal vaccinations for pertussis should be encouraged.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13052-023-01495-8.