This study aimed to compare the risk of chronic periodontitis (CP) between participants who underwent tonsillectomy and those who did not (control participants) using a national cohort dataset. Patients who underwent tonsillectomy were selected from a total of 514,866 participants. A control group was included if participants had not undergone tonsillectomy from 2002 to 2015. The number of CP treatments was counted from the date of the tonsillectomy treatment. Patients who underwent tonsillectomy were matched 1:4 with control participants who were categorized based on age, sex, income, and region of residence. Finally, 1044 patients who underwent tonsillectomy were matched 1:4 with 4176 control participants. The adjusted estimated value of the number of post-index date (ID) CP did not reach statistical significance in any post-ID year (each of p > 0.05). In another subgroup analysis according to the number of pre- ID CP, it did not show statistical significance. This study revealed that tonsillectomy was not strongly associated with reducing the risk of CP. Even though the tonsils and periodontium are located adjacently, and tonsillectomy and CP may be related to bacterial inflammation, there was no significant risk of CP in patients undergoing tonsillectomy.