We previously demonstrated that PDZRN3, an E3 ubiquitin ligase, is essential for myogenic differentiation from myoblasts to myotubes. In regeneration of injured skeletal muscle in vivo, the expression of MyoD is induced in stem cells and these differentiated cells (myoblasts) expand through proliferation. We reported that PDZRN3 is upregulated along with MyoD during regeneration of injured muscle. In this study, we aimed to clarify a role of PDZRN3 in proliferation of myoblasts. When exposed to starvation stress, PDZRN3-depleted C2C12 myoblasts by RNAi showed higher levels of apoptotic markers as compared with those of control cells. On the other hand, PDZRN3-depletion suppressed the activation of anti-apoptotic Akt, indicating the involvement of PDZRN3 in apoptotic regulation. In addition, we found that the expression of cyclin A2, a direct activator of Akt, was reduced in PDZRN3-depleted cells. Cyclin A2 directly activates the translation of DNA repair factor Mre11. In fact, the expression of Mre11 was decreased in the PDZRN3-depleted cells, and the activation of p53 was enhanced in these cells probably due to the DNA damage accumulation. These results indicate that PDZRN3 plays an important role in apoptotic regulation of myoblasts, modulating the expression of cyclin A2.