Objective We aimed to investigate the annual prevalence of intellectual disabilities (ID) and autism spectrum disorder employing claims data registered in Korean National Health Insurance Service. We also estimated the annual average of medical costs incurred from these disorders using same datasets. Methods In order to obtain the prevalence, we selected patients diagnosed with ID and pervasive and specific developmental disorders (PDD) from 2007 to 2019. The ensuing annual average of medical costs was also estimated from these patients. Results The annual prevalence of ID and PDD (per 100,000) between 2007 and 2019 ranged from 56.7 to 78.6 and from 22.0 to 44.6 respectively. Regarding the annual average of total medical expenditure per a patient, the expenditure of the ID group was higher than that of PDD throughout the years, as shown that the ID expenditure ranged from 769.7 to 1,501.2 US dollars as opposed to the PDD expenditure in the range of 312.5 to 570.7 US dollars. The further comparison in relation to income levels elaborated that the medical aid beneficiary group constitutes the highest one and the difference of the expenditure across the remaining income groups was not prominent although the very low group generally ranked the highest over the years. Conclusion The prevalence of ID and PDD constantly increased and the same trend was displayed in ensuing health expenditures throughout the period. This implies that increasing needs exist across these patients with regards to therapeutic interventions, thereby contributing to prioritizing medical policies on national perspectives.