Epidemiological data of rare diseases are important for understanding disease burden, improving treatment, and planning healthcare systems. However, those of acromegaly in Japan are not well known. Our study aimed to describe the prevalence, incidence, prediagnostic comorbidities, and treatment patterns of patients with acromegaly in Japan. Using the National Database of Health Insurance Claims and Specific Health Checkups of Japan, we retrospectively identified 12,713 patients with acromegaly aged ≥20 years between January 2014 and December 2017 (the prevalence cohort), 2,552 newly diagnosed patients between January 2013 and December 2017 (the incidence and comorbidity cohort), and 2,125 patients enrolled in the database at least 365 days after the diagnosis (the treatment-pattern cohort). The average annual prevalence in 2015-2017 was 9.2 cases per 100,000 in the prevalence cohort, and the average annual incidence in 2013-2017 was 0.49 cases per 100,000 in the incidence and comorbidity cohort. The most common prediagnostic comorbidities included hypertension (43%), diabetes (37%), and hyperlipidemia (27%). In the treatment-pattern cohort, 54% and 45% of patients received surgery and medical treatment as the primary treatment, respectively. Between the first surgery and 365 days after diagnosis, 15% of the patients in this cohort received medical treatment as the secondary treatment, mostly with somatostatin analogs (83%). Of the 1,569 patients who underwent surgery, 29% received medical treatment before surgery. The prevalence and incidence of acromegaly in Japan were similar to those in other countries. This epidemiological study provides the basis for better management of acromegaly nationwide.