Purpose <p>Understanding the incidence of rare diseases is important in establishing a proper public health care system and setting target diseases in medical research. Herein, we report the 12-year cumulative incidence of seven rare ocular diseases of the retina in South Korea.</p> Methods <p>We analysed clinical records of 1,126,250 South Korean population during 2006~2019. We conducted a nationwide, population-based, cohort study using data from the Korean National Health Claims database. With codes in the Korean Standard Classification of Diseases, the cumulative incidence of each retinal disease (Choroideremia, Eales disease, Coats disease, Retinitis pigmentosa, Best disease, Stargardt disease, and Leber’s congenital amaurosis) was calculated. Incidences in different sex and age groups were also assessed.</p> Results <p>Late-onset diseases had a higher incidence rate in adulthood, but there were no definite differences between sex. The 12-year cumulative incidence per 100,000 people in rare retinal diseases was 0.66 to 28.45. Among them, retinitis pigmentosa revealed higher incidence (28.45 (95% CI 25.59–31.30) in total, 29.33 (95% CI 23.67–34.99) in males, 29.47 (95% CI 25.38–33.55) in female). Late-onset rare retinal diseases such as Eales diseases and Best diseases have higher incidence rates in adults. The incidence difference according to gender was not significant.</p> Conclusions <p>This study determined the estimated long-term cumulative incidence rate of rare retinal diseases and the distribution of the incidence based on sex and age. The nationwide epidemiological data would give useful information for public health and further research.</p>