Several private boarding schools in England have established universal influenza vaccination programmes for their pupils. We evaluated the impact of these programmes on the burden of respiratory illnesses in boarders. Between November 2013 and May 2014, age-specific respiratory disease incidence rates in boarders were compared between schools offering and not offering influenza vaccine to healthy boarders. We adjusted for age, sex, school size and week using negative binomial regression. Forty-three schools comprising 14 776 boarders participated. Almost all boarders (99%) were aged 11–17 years. Nineteen (44%) schools vaccinated healthy boarders against influenza, with a mean uptake of 48·5% (range 14·2–88·5%). Over the study period, 1468 respiratory illnesses were reported in boarders (5·66/1000 boarder-weeks); of these, 33 were influenza-like illnesses (ILIs, 0·26/1000 boarder-weeks) in vaccinating schools and 95 were ILIs (0·74/1000 boarder-weeks) in non-vaccinating schools. The impact of vaccinating healthy boarders was a 54% reduction in ILI in all boarders [rate ratio (RR) 0·46, 95% confidence interval (CI) 0·28–0·76]. Disease rates were also reduced for upper respiratory tract infections (RR 0·72, 95% CI 0·61–0·85) and chest infections (RR 0·18, 95% CI 0·09–0·36). These findings demonstrate a significant impact of influenza vaccination on ILI and other clinical endpoints in secondary-school boarders. Additional research is needed to investigate the impact of influenza vaccination in non-boarding secondary-school settings.