The absence of dystrophin has gave a massive impact on myotube development in Muscular Dystrophy pathogenesis. One of the conserved signalling pathways involved in skeletal muscle differentiation is the PI3K/Akt/mTOR pathway that play a vital role in autophagy regulation. To further understand and establish targeted therapy in dystrophin-deficient myoblasts, protein expression profiling has been determined which provides information on perturbed autophagy modulation and activation. In this study, dystrophin-deficient myoblast cell line established from skeletal muscle of dystrophic (mdx) mouse were used as model. The dfd13 (dystrophin-deficient) and C2C12 (non-dystrophic) myoblasts were cultured in low mitogen conditions for 10 days to induce differentiation. The cells were subjected to total protein extraction prior to western blotting assay technique. Protein sub-fractionation has been conducted to determine protein localisation. The live cell analysis of autophagy assay were done using flow cytometer. As results, in our culture system, the dfd13 myoblasts did not achieved terminal differentiation. PTEN expression was profoundly increased in dfd13 myoblasts throughout the differentiation day subsequently imposed perturbation of PI3K/Akt/mTOR regulation. In addition, rictor-mTORC2 was also found inactivated in this event. This occurrence has caused FoxO3 misregulation resulting higher activation of autophagy related genes in dfd13 myoblasts. Autophagosome formation was increased as LC3B-I/II showed accumulation upon differentiation. However, ratio of LC3B lipidation and autophagic flux were shown decreased which exhibited dystrophic features. As a conclusion, perturbation of the PTEN-PI3K/Akt pathway triggers excessive autophagosome formation, and subsequently reduced autophagic flux within dystrophin-deficient myoblasts where this finding are of important to understand DMD patients which fit with the actual scenario. We believe that some manipulation within its regulatory signalling reported in this study could help restore muscle homeostasis and attenuate disease progression.