Abstract Background Juvenile systemic sclerosis (jSSc) can lead to permanent and irreversible anatomical or physiological dysfunction. The Scleroderma Clinical Trials Consortium-Damage Index (SCTC-DI), which has been employed and validated in adult patients, can quantify organ damage and predict mortality and morbidity. However, its application in paediatric patients remains unexplored. Methods Clinical data, laboratory results, and prognostic information were collected for patients with jSSc at Peking Union Medical College Hospital (PUMCH) from January 2012 and January 2024. Differences between the SCTC-DI and the juvenile systemic sclerosis severity score (J4S) were recorded and compared. Furthermore, we compared the SCTC-DI between jSSc and adult systemic sclerosis (SSc) patients. Results A total of 64 jSSc patients were included. Facet joint contractures, fingertip ulcers and interstitial lung disease are common manifestations. Compared with adult SSc patients, jSSc patients had a lower incidence of gastrointestinal and urinary system involvement. The baseline J4S levels were significantly correlated with SCTC-DI levels at follow-up. A higher baseline SCTC-DI score was associated with a greater progression of organ damage (P = 0.001). Conclusion There are differences in clinical presentations between adult SSc patients and jSSc patients. The SCTC-DI can be applied to JSSc patients, and it is recommended that JSSc patients undergo regular evaluations of the J4S as well as the SCTC-DI.