Background: Carpal tunnel syndrome is rare in the paediatric population but is frequently associated with mucopolysaccharidosis. Owing to nonspecific symptoms and limited reliability of clinical examination, early diagnosis of carpal tunnel syndrome in patients with mucopolysaccharidosis remains challenging. Advanced ultrasonographic techniques may enable objective and early detection. Objective: To evaluate the diagnostic performance of ultra-microangiography and shear wave elastography for the early detection of carpal tunnel syndrome in pediatric patients with mucopolysaccharidosis and to investigate their potential contribution to existing diagnostic protocols. Materials and methods: This cross-sectional study included 44 individuals (mean age, 11.6±4.8 years), comprising 22 pediatric patients with genetically confirmed mucopolysaccharidosis and 22 age- and sex-matched healthy controls. The mucopolysaccharidosis group was further divided into carpal tunnel syndrome–negative (n=16) and carpal tunnel syndrome–negative (n=6) subgroups based on electromyography. Median nerve cross-sectional area, vascular index obtained by ultra-microangiography, and stiffness values measured by shear wave elastography (expressed in kilopascals) were evaluated bilaterally. Diagnostic performance was assessed using receiver operating characteristic analysis. Results: Significant differences were observed among control, carpal tunnel syndrome-negative mucopolysaccharidosis, and carpal tunnel syndrome-positive mucopolysaccharidosis groups for median nerve cross-sectional area, vascular index, and stiffness values (all P<0.001). These parameters demonstrated high diagnostic performance in distinguishing mucopolysaccharidosis patients from healthy controls, with area under the curve values ranging from 0.853 to 1.000. Among mucopolysaccharidosis patients, these parameters also demonstrated high accuracy in differentiating carpal tunnel syndrome-positive from carpal tunnel syndrome-negative individuals (AUC, 0.891–0.984), with sensitivity ranging from 83.3% to 100% and specificity from 87.5% to 93.7%. Conclusion: Our findings suggest that ultra-microangiography and shear wave elastography may provide complementary quantitative information for the evaluation of early median nerve changes in pediatric patients with mucopolysaccharidosis, although further studies are required to validate the clinical utility of shear wave elastography in peripheral nerves.