Background While the burden of community‐acquired pneumonia and invasive pneumococcal disease ( IPD ) is still considerable, there is little insight in the factors contributing to disease. Previous research on the lagged relationship between respiratory viruses and pneumococcal disease incidence is inconclusive, and studies correcting for temporal autocorrelation are lacking. Objectives To investigate the temporal relation between influenza‐like illnesses ( ILI ) and IPD , correcting for temporal autocorrelation. Methods Weekly counts of ILI were obtained from the Sentinel Practices of NIVEL Primary Care Database. IPD data were collected from the Dutch laboratory‐based surveillance system for bacterial meningitis from 2004 to 2014. We analysed the correlation between time series, pre‐whitening the dependent time series with the best‐fit seasonal autoregressive integrated moving average ( SARIMA ) model to the independent time series. We performed cross‐correlations between ILI and IPD incidences, and the (pre‐whitened) residuals, in the overall population and in the elderly. Results We found significant cross‐correlations between ILI and IPD incidences peaking at lags ‐3 overall and at 1 week in the 65+ population. However, after pre‐whitening, no cross‐correlations were apparent in either population group. Conclusion Our study suggests that ILI occurrence does not seem to be the major driver of IPD incidence in The Netherlands.