Since implementation of the International Statistical Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) in the US, thousands of new or related codes have been added to represent clinical conditions. The widely used pediatric complex chronic condition (CCC) system required a major update from version 2 (V2) to version 3 (V3) to capture the range of clinical conditions represented in the ICD-10-CM. To update the CCC V3 system, creating V3, with new, missing, or retired codes; to reconceptualize the system's use of technology codes; and to compare CCC V3 with V2. This repeated cross-sectional study examined US hospitalization data from the Pediatric Health Information System (PHIS) and the Medicaid Merative MarketScan Research Databases from January 1, 2009, to December 31, 2019, for all patients aged 0 to 18 years. Data were analyzed from March 1, 2023, to April 1, 2024. The CCCs were identified in both data sources using the CCC V2 and V3 systems. The (1) percentage of pediatric hospitalizations associated with a CCC, (2) numbers of CCC body-system categories per patient, and (3) explanatory power for hospital length of stay and in-hospital mortality were compared over time for V3 vs V2. Among 7 186 019 hospitalizations within PHIS, 54.3% patients were male, the median age was 4 years (IQR, 1-11 years), and 51.2% were aged 0 to 4 years). The CCC V2 identified 2 878 476 (40.1%) patients as having any CCC compared with 2 753 412 (38.3%) identified by V3. In addition, V2 identified 100 065 (1.4%) patients with transplant status compared with 146 683 (2.0%) by V3, and V2 identified 914 835 (12.7%) as having technology codes compared with 805 585 (11.2%) by V3. The 2 systems were similar in accounting for the number of CCC body-system categories per patient and in explaining variation in hospital length of stay and in-hospital mortality. For both V2 and V3, 10.0% of the variance in hospital length of stay and 12.0% of the variance in in-hospital mortality was explained by the presence of a CCC. Similar patterns were observed when analyzing the 2 999 420 Medicaid Merative MarketScan Research Databases' hospitalizations (52.3% of patients were male, the median age was 1 year [IQR, 0-12 years], and 62.0% were 0 to 4 years old), except that the percentages of identified CCCs were all lower: V2 identified 758 110 hospitalizations (25.3%) with any CCC compared with 718 100 (23.9%) identified by V3. These results suggest that, moving forward, V3 should be used to identify CCCs, and ongoing, frequent updates to V3, using a transparent, structured process, will enable V3 to accurately reflect the evolving spectrum of clinical conditions represented in the ICD-10-CM.