Aims Beta‐blockers are commonly used to treat hypertension that arises during pregnancy. However, reproductive safety concerns have been expressed. Here, we investigated whether the use of β‐blockers during early pregnancy increased the risk of congenital malformations. Methods A systematic literature search was performed in PubMed, Embase and Cochrane Library to identify relevant studies published from database inception until February 2020. Observational studies evaluating associations between maternal β‐blocker use and congenital malformations were included in this meta‐analysis. Two reviewers independently extracted data and assessed study quality. Meta‐analysis of outcomes was performed and a summary odds ratio (OR) was calculated with consideration of heterogeneity. Results Twenty observational studies were identified. Beta‐blocker use during early pregnancy was not associated with an increased risk of congenital malformations (OR = 1.01, 95% confidence interval [CI] = 0.93–1.09). Subgroup analysis of organ‐specific malformations revealed that β‐blocker use was associated with an increased risk of heart malformations (OR = 1.29, 95% CI = 1.02–1.63) and an increased risk of cleft lip or palate (OR = 1.5, 95% CI = 1.18–1.91); however, these associations (OR = 1.11, 95% CI = 0.94–1.32 for heart malformations; OR = 1.34, 95% CI = 0.98–1.85 for cleft lip or palate) disappeared when the adjusted data were pooled. Beta‐blocker use was not associated with increased risks of central nervous system malformations, neural tube defects or hypospadias. Conclusion Exposure to β‐blockers during early pregnancy does not appear to be associated with congenital malformations or heart malformations in offspring. Other organ‐specific congenital malformations should be evaluated in further studies.