ObjectivesPregnant women are among the priority groups to receive influenza vaccines in the Czech Republic since 2011, data on vaccination coverage are not yet available. The aim of the study was to determine the influenza vaccination coverage (IVC) and provide source data for further activities.MethodsA prospective observational study was performed in a large maternity hospital in Prague. The self-completed questionnaire was distributed to 5,475 pregnant women between September 1, 2020 and August 31, 2021. Questions included maternal sociodemographic characteristics, influenza vaccination status and sources of maternal vaccination recommendations during pregnancy.ResultsA total of 4,617 completed questionnaires have been analysed. The median age of study participants (N = 4,592) was 33 years (range: 18–51 years). The majority (69.7%) of women had completed their university education, most women were childless (58.5%) or had one child (32.5%) before the start of the study. Less than 2% of women reported being vaccinated against influenza during their pregnancy (1.5%; 95% CI, 1.1–1.9%). Only 21% of women knew that it’s possible to get vaccinated against influenza during pregnancy. Participants considered influenza vaccination in pregnancy as important (3.3%), useful (41.1%) and useless (44.4%). Out of 959 pregnant women who had information about influenza vaccination during pregnancy, only 6.9% were vaccinated, while among those who did not have this information, 0.1% were vaccinated during pregnancy (p < 0.001). The most frequent source of information was Internet, then media and a general practitioner.ConclusionsThe IVC during pregnancy in our study was extremely low. In order to improve IVC among pregnant women, it is necessary to increase awareness of recommendations and vaccination options among the public and professionals and incorporating vaccination recommendation in routine antenatal practice.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-15911-5.