Background Infants with influenza, particularly those younger than 1 year of age, are at high risk of developing a severe case or of dying. Recently, owing to the spread of pandemic influenza A (H1N1) 2009, the Advisory Committee on Immunization Practices recommended maternal immunization to reduce the risk of influenza infection in pregnant women and infants. Such reporting is rare in Japan. The aim of this study was therefore to investigate the effect on the newborn of influenza vaccination of pregnant women in Japan. Methods The study included 200 infants who were born to healthy mothers at Kobayashi Ladies Clinic during influenza season from November 2010 to April 2011. The incidence of fever and laboratory‐confirmed influenza was assessed in the infants for the 6 months after their birth. Results Of the 200 infants, four were excluded from this study due to loss to follow up. The 106 infants in the group whose mothers received the influenza vaccine (vaccinated group) before parturition were compared with the 90 infants in the group whose mothers did not receive the influenza vaccine (non‐vaccinated group). Fever was noted in 36 infants (34.0%) in the vaccinated group and in 47 infants (52.2%) in the non‐vaccinated group (P < 0.007), and the incidence of influenza was 0 (0%) and 5 (5.6%), respectively (P = 0.019). The incidence of fever and influenza among infants was significantly lower in the vaccinated group compared with the non‐vaccinated group. Conclusions Maternal influenza immunization should be actively recommended in Japan to protect newborns from influenza viruses.