Human bocaviruses (HBoVs) are recently described as human emergent viruses, especially in young children. In this study, we undertook a systematic review and meta‐analysis to estimate their prevalence in Europe. PubMed, Web of Science and Scopus databases were systematically screened for clinical studies, up to October 2020. Study eligibility criteria were primary full‐text articles from clinical studies, conducted using valid screening test methods and published in peer‐reviewed journals, in English or Spanish and from European countries. The overall pooled prevalence, prevalence by country as well as the prevalence of HBoV as a single or co‐pathogen were estimated using a random‐effects model. Sub‐group and meta‐regression analyses explored potential sources of heterogeneity in the data. A total of 35 studies involving 32,656 subjects from 16 European countries met the inclusion criteria. Heterogeneity (I2 = 97.0%, p <.01) was seen among studies; HBoV prevalence varied from 2.0 to 45.69% with a pooled estimate of 9.57% (95%CI 7.66‐11.91%). The HBoV prevalence both as a single infection (3.99%; 95%CI 2.99‐5.31%) or as co‐infection with other viruses (5.06%; 95%CI 3.88‐6.58%) was also analysed. On a geographic level, prevalence by country did not show statistical differences, ranging from 3.24% (Greece) to 21.05% (Denmark). An odds ratio analysis was also included in order to evaluate the relevance of the variable 'age' as a risk factor of HBoV infection in children <5 years old. The OR value of 1.77 (95%CI 1.13‐2.77; p <.01) indicated that being <5 years old is a risk factor for HBoV infection. This study showed that HBoV has a moderate prevalence among European countries. [ABSTRACT FROM AUTHOR]