Pneumonia and sepsis are invasive diseases caused by Streptococcus Pneumoniae. These incidences increase every year with high mortality and morbidity. As the incidence of invasive diseases increases, the economic expense caused by the treatment also increases. The aims of this study were to determine the cost of invasive diseases treatment which includes direct medical cost, direct nonmedical cost, and indirect cost as well as direct medical cost along with the comparison of INA-CBG's fare according to Permenkes RI No.64/2016 on pediatric inpatients in RSUD Sleman. The study used observational method with cross sectional design, following the societal perspective. Data collection, started from September 2017 to March 2018 was conducted prospectively by interviewing the patient’s parent using questionnaires, as well as searching for medical record and cost of treatment of invasive diseases of pediatric inpatients data that fulfill inclusion requirement of the research in RSUD Sleman. The data were analysed using the descriptive method with 59 pneumonia patients and 1 sepsis patient, while the comparison of direct medical cost with INA-CBG's fare used statistical test method with independent t-test and Mann Whitney. Pneumonia patients with J-4-16-I code were 29 patients, J-4-16-II code was 4 patients, J-4-16-III code was 2 patients and 1 patient sepsis with code A-4-10-III. Cost of illness in invasive diseases pediatric inpatients which includes direct medical cost, direct nonmedical cost and indirect cost is Rp187.024.979, with the largest component is direct medical cost. Comparison of direct medical cost with INA-CBG's fare has p-value 0 in patients with pneumonia. These results indicate that there are significant differences with INA-CBG's fare are greater than direct medical costs.