Invasive diseases consist of pneumonia, sepsis, and meningitis which are caused by Streptococcus pneumonia (pneumococcus) bacterium. Every year, the death of infants and toddlers caused by pneumonia has always ranked at the top in Indonesia. As the incidence of invasive diseases increases each year, it will also increase the economic burden that will be issued. This study aims to determine the cost of invasive diseases treatment which includes direct medical cost, direct nonmedical cost, and indirect cost, and direct medical cost comparison with INA-CBG's fare based on Permenkes RI No. 64 year 2016 on pediatric inpatients at RSUD Panembahan Senopati Bantul. The type of this research is observational with cross sectional study design according to societal perspective. The data collection method had been done prospectively by interviewing the parents of the patients using questionnaires. Medical record and cost of treatment of invasive diseases inpatient data fulfilling the inclusion criteria were also used to collect data. The data had been analyzed using descriptive statistic analysis method with 48 patients with pneumonia and 4 patients with sepsis. The comparison of direct medical cost with INA-CBG's fare based on Permenkes RI No. 64 year 2016 were analyzed using independent t test statistical test for normal data and mann-whitney statistical test for abnormal data. The total cost of illness of invasive diseases including direct medical cost, direct non medical cost, and indirect cost is Rp164,631,963 with average is Rp3,165.999 ± 1,008.489. The largest component is direct medical cost, mainly the cost of drugs and medical devices. For comparison with INA-CBG's fare, the analysis obtained p value 0,000 for patients with pneumonia. It can be concluded that direct medical cost and INA-CBG's fare have significant differences with INA-CBG's fare is greater than the real cost.