The complexity of RNA metabolism has become crucial in neuromuscular diseases, especially for Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Our goal was to search for possible pathways that differ between the two diseases, in which DMD develops a severe phenotype compared to BMD. In this work, we aimed to evaluate the transcriptomic profile in skeletal muscle biopsies derived from patients with either DMD or BMD. We collected RNA obtained from pediatric patients with DMD (n = 12) and with BMD (n = 6). Compared to patients with BMD, patients with DMD showed a particular activation of genes involved in collagen synthesis, extracellular matrix organization, and Oncostatin M-dependent pathways, important for fibrotic processes. This suggests that a more severe phenotype in patients with DMD compared to those with BMD may be due to greater deregulation of these pathways, reflecting the clinical picture of patients observed. Our results allowed us to highlight the molecular differences between the two phenotypic groups, shedding light on the pathways that make Duchenne dystrophy more severe than its counterpart does. This study provides preliminary insights into the difference in gene expression between the two groups and lays the basis for the identification of possible mechanisms that differentiate between the two diseases.