This study evaluates the influenza vaccine effectiveness (VE) in preventing laboratory-confirmed cases in Navarre, Spain, in the 2011/12 season in which the peak was delayed until week 7 of 2012. We conducted a test-negative case–control study. Patients with influenza-like illness in hospitals and primary healthcare were swabbed for testing by reverse transcription-polymerase chain reaction. Influenza vaccination status and other covariates were obtained from healthcare databases. The vaccination status of confirmed cases and negative controls was compared after adjusting for potential confounders. VE was calculated as (1-odds ratio)x100. The 411 confirmed cases (93% influenza A(H3)) were compared with 346 controls. Most characterised viruses did not match the vaccine strains. The adjusted estimate of VE was 31% (95% confidence interval (CI): -21 to 60) for all patients, 44% (95% CI: -11 to 72) for those younger than 65 years and 19% (95% CI: -146 to 73) for those 65 or older. The VE was 61% (95% CI: 5 to 84) in the first 100 days after vaccination, 42% (95% CI: -39 to 75) between 100 and 119 days, and zero thereafter. This decline mainly affected people aged 65 or over. These results suggest a low preventive effect of the 2011/12 seasonal influenza vaccine, and a decline in VE with time since vaccination.