Introduction: Vaccine-preventable diseases such as pertussis are re-emerging in Malaysia during recent years. Objective: This research aims to study the local incidence of clinical pertussis among paediatric patients admitted to Hospital Tuanku Fauziah, Perlis over two-year period. Method: A cross-sectional study was designed in Department of Paediatrics, Hospital Tuanku Fauziah, Perlis from 1 January 2013 till 31 January 2015. Data were collected from medical and laboratory record of cases admitted for clinical pertussis. Analyses for descriptive data were done using frequency and percentage; Pearson chi-square or Fisher exact was used to test association. Results: 81 cases of clinical pertussis were included in the study. Out of this, there were a total of 28 confirmed cases of pertussis. There was a steady increment in the incidence of pertussis throughout the study period. Cyanosis emerged as the only clinical sign significantly associated with pertussis (p = 0.011). Majority of the confirmed pertussis cases were too young to be immunized (n = 13, 46.4%). Conclusion: Reappraisal of local health system to strengthen herd immunity in the community is warranted to control disease spread.