Objectives: During recent decades, there has been limited attention on the seasonal pattern of pertussis within a high vaccine coverage population. This study aimed to compare the seasonal patterns of clinical suspected pertussis cases with those of laboratory confirmed cases in Iran. Methods: The current study was conducted using time series methods. Time variables included months and seasons during 2011–2013. The effects of seasons and months on the incidence of pertussis were estimated using analysis of variance or Kruskal–Wallis. Results: The maximum average incidence of clinically confirmed pertussis was 23.3 in July (p = 0.04), but the maximum incidence of clinical suspected pertussis was 115.7 in May (p = 0.6). The maximum seasonal incidences of confirmed and clinical pertussis cases were reported in summer (average: 12, p = 0.004), and winter (average: 108.1; p = 0.4), respectively. Conclusion The present study showed that the seasonal pattern of laboratory confirmed pertussis cases is highly definite and different from the pattern of clinical suspected cases.