Pregnant women have a high risk of severe influenza, associated with obstetrical complications. The World Health Organization (WHO) has recommended influenza vaccination for all pregnant women since 2012. The vaccination coverage remains low worldwide, and in Europe, due to a lack of proposition from the health care providers, and a high refusal rate from the women. The primary aim of this study was to estimate the influenza vaccination coverage (IVC) in a population of pregnant women in France, and to analyse its evolution from 2009 to 2018. The secondary objective was to describe the vaccinated population and to find determinants associated with the vaccination. This retrospective cohort study is based on the EGB French health care database, a representative sample of the French population containing data from the health insurance system. All pregnant women who delivered medically or spontaneously over the 2009–2018 period were included. In the 2009–2018 period, only 1.2% pregnant women were vaccinated against influenza (n = 875/72,207; 95% CI 1.14–1.30). The IVC slightly increased after the 2012 WHO recommendation, from 0.33 to 1.79% (p < 0.001) but remained extremely low (4.1% in 2018). Women younger than 25 years old had a low coverage (0.6%) whereas women over 35 years old were more likely to get the influenza vaccine (1.7%; OR: 2.82, 95% CI 2.14–3.71). The vaccination behavior was not influenced by multifetal pregnancy or parity, but socio-economically deprived women were less likely to be vaccinated (OR: 0.81, 95% CI: 0.67–0.98). Women with pre-existing medical conditions had an overall higher vaccination rate (2.5%; OR: 2.32, 95% CI: 1.94–2.77). The vaccine was mainly prescribed by family physicians (58%). Influenza vaccination in pregnant women in France remains very low, particularly in younger, healthy women, and measures such as information campaigns towards pregnant women and studies of the knowledge, attitudes, and practices of the health care professionals need to be undertaken to improve the coverage.