Hidradenitis suppurativa (HS), also called acne inversa, is an inflammatory skin disease, which causes HS patients to suffer from recurrent symptoms and severe comorbidities. The aim of this article was to provide evidence on the epidemiology of HS in Taiwan through a retrospective population‐based cohort study. The patients with International Classification of Diseases, Ninth Revision, Clinical Modification code 705.83 and Anatomical Therapeutic Chemical codes for HS treatments from 2000 to 2013 in the National Health Insurance Research Database, which covers 99.9% Taiwanese residents, were enrolled in this 14‐year nationwide population‐based cohort study. The age‐ and sex‐standardized prevalence, incidence, and the prescription pattern for HS were analyzed. The annual percent change (APC) was used to estimate the trend of prevalence and incidence of HS from 2000 to 2013. During 2000–2013 in Taiwan, the 14‐year period prevalence rate was 185.6/100 000 (95% confidence interval [CI], 177.3–194.3) with an APC of –2.96% (95% CI, −1.73 to −4.17) and the mean annual adjusted incidence rate from 2001 to 2013 was 11.8/100 000 (95% CI, 11.2–12.5) with an APC of −4.65% (95% CI, −3.32 to −5.95). Female : male ratio was 0.92 and the most common onset age was 15–24 years. Major treatments were systemic corticosteroids, systemic antihistamines, systemic antibiotics, and topical antibiotics. An increasing tendency of using systemic antibiotics was noted. In Taiwan, decreasing incidence and prevalence of HS was shown during 2000–2013. Relatively lower incidence and prevalence were noted compared to Western countries. Male predominance was revealed, and the use of systemic antibiotics became the mainstream in treatment for HS.