Hidradenitis suppurativa (HS) is associated with various metabolic and autoimmune diseases. The epidemiology has been analyzed in various studies worldwide. However, epidemiological data on HS for Asian populations are limited. This study aimed to analyze the change in the prevalence and incidence of HS over 17 years in South Korea using the Korean National Health Insurance Service (NHIS) database. This study also evaluated the comorbidities in patients with HS. Population-based data from the NHIS database of Korea were obtained between January 2003 and December 2019. Odds ratios were estimated to determine the association between comorbidities and HS during the study period. Hazard ratios for the risk of incident comorbidities in patients with HS were obtained using the multivariable Cox proportional hazard analysis. This study included 45 511 patients with HS and 910 220 controls matched for age, sex, insurance type, and income level. The incidence rate of HS per 1 000 000 person-years in Korea increased from 11.69 in 2003 to 78.78 in 2019. The annual prevalence per 1 000 000 people also increased from 34.68 in 2003 to 140.10 in 2019, showing a similar trend. Many comorbidities, including atopic, metabolic and end-organ, autoimmune/inflammatory, and psychiatric diseases were associated with HS at baseline. In many diseases, the risk of incident comorbidities in patients with HS was higher than that in controls. The incidence and prevalence of HS in Korea have increased over the past 17 years. Various comorbidities, including allergic diseases, hypertension, diabetes mellitus, dyslipidemia, myocardial infarction, chronic hepatitis and cirrhosis, chronic kidney disease, inflammatory bowel diseases, rheumatoid arthritis, vitamin D deficiency, and psychiatric diseases, were associated with HS. Physicians need to keep in mind and closely monitor these comorbidities in patients with HS.