Bordetella pertussis (B. pertussis) is the causative agent of pertussis, also referenced as whooping cough. Although pertussis has been appropriately controlled by routine immunization of infants, it has experienced a resurgence since the beginning of the 21st century. Given that elucidating the immune response to pertussis is a crucial factor to improve therapeutic and preventive treatments, we re-analyzed a time course microarray dataset of B. pertussis infection by applying a newly developed dynamic data analysis pipeline. Our results indicate that the immune response to B. pertussis is highly dynamic and heterologous across different organs during infection. Th1 and Th17 cells, which are two critical types of T helper cell populations in the immune response to B. pertussis, and follicular T helper cells (TFHs), which are also essential for generating antibodies, might be generated at different time points and distinct locations after infection. This phenomenon may indicate that different lymphoid organs may have their unique functions during infection. These findings provide a better understanding of the basic immunology of bacterial infection, which may provide valuable insights for the improvement of pertussis vaccine design in the future.