The burden of fungal diseases based on the real-world national data is limited. This study aimed to estimate the Taiwan incident cases with selected fungal diseases in 2013 using the National Health Insurance Research Database (NHIRD) which covered 99.6% of the 23.4 million population. Over 80,000 incident cases were found and the majority were superficial infections including vulvovaginal candidiasis (477 per 100,000 adult women) and oral candidiasis (90 cases per 100,000 population). Common potentially life-threating fungal diseases were Pneumocystis pneumonia (5.35 cases per 100,000 population), candidemia (3.68), aspergillosis (2.43) and cryptococcal meningitis (1.04). Of the aforementioned cases cancer patients contributed 30.2%, 42.9%, 38.6% and 22.2%, respectively. Of 22,270 HIV-infected persons in NHIRD in 2013, four common diseases were Pneumocystis pneumonia (28.3 cases per 1000 HIV-infected patients), oral candidiasis (17.6), esophageal candidiasis (6.06) and cryptococcal meningitis (2.29). Of pulmonary aspergillosis 32.9% occurred in patients with chronic pulmonary diseases and 26.3% had a prior diagnosis of tuberculosis. There are some notable gaps related to insurance claim data. Cutaneous, urinary tract and eye fungal infections were not captured.