Background Recent studies have suggested that vaccination with seasonal influenza vaccine resulted in an apparent higher risk of infection with pandemic influenza H1N1 2009. A simple mathematical model incorporating strain competition and a hypothesised temporary strain-transcending immunity is constructed to investigate this observation. The model assumes that seasonal vaccine has no effect on the risk of infection with pandemic influenza. Results Results of the model over a range of reproduction numbers and effective vaccination coverage confirm this apparent increased risk in the Northern, but not the Southern, hemisphere. This is due to unvaccinated individuals being more likely to be infected with seasonal influenza (if it is circulating) and developing hypothesised temporary immunity to the pandemic strain. Because vaccinated individuals are less likely to have been infected with seasonal influenza, they are less likely to have developed the hypothesised temporary immunity and are therefore more likely to be infected with pandemic influenza. If the reproduction number for pandemic influenza is increased, as it is for children, an increase in the apparent risk of seasonal vaccination is observed. The maximum apparent risk effect is found when seasonal vaccination coverage is in the range 20-40%. Conclusions Only when pandemic influenza is recently preceded by seasonal influenza circulation is there a modelled increased risk of pandemic influenza infection associated with prior receipt of seasonal vaccine.