Background: Stroke occurrence appears to be a random event, yet annual and supra-annual periodicity is observed. Recent attention in atherosclerotic disease etiology has focused on infectious and inflammatory mechanisms. Influenza is one such infection that may influence stroke occurrence. Methods: We explored population-based time series data on stroke occurrence and influenza activity. Using Fourier transformation to isolate low-frequency signals in the data, the inverse transformed time series were regressed using Prais-Winsten regression to correct for serially auto-correlated residuals, to assess the relationship between influenza rates and stroke occurrence rates. Results: Changes in the low-frequency components of influenza activity predicted the changes in low-frequency components of the stroke occurrence data with a delay of about 20 weeks. The delay between changes in influenza activity and subsequent stroke activity was different for different stroke types. Overall, the effect size was small with a tripling of the influenza rate associated with about a 6% change in stroke occurrence rate. Conclusions: A small proportion of the patterns of stroke occurrence may be explained by variation in influenza activity. Further evaluation of influenza as a triggering agent in stroke is needed.