The economic effects of pandemic influenza, a regularly recurring form of infectious disease, are analysed. Epidemiological and economic models are linked to capture the transmission of the pandemic from regional populations to regional economies. The analysis builds on previous studies that apply computable general equilibrium models with quarterly periodicity to assess the economic effects of infectious disease. The economic effects are assessed with the annual and quarterly periodicity, and the results are compared and contrasted. The analysis demonstrates the importance of quarterly periodicity as it can capture the short, sharp duration of influenza pandemics. The results demonstrate that annual economic models strongly underestimate the economic effects of infectious disease outbreaks that have a lifespan of less than one year because they can not accurately capture the time profile of an infectious disease outbreak.