Autophagy is a conserved cellular process for degrading aggregate proteins and dysfunctional organelle. It is still debatable if autophagy and mitophagy (a specific process of autophagy of mitochondria) play important roles in myogenic differentiation and functional regeneration of skeletal muscle. We tested the hypothesis that autophagy is critical for functional regeneration of skeletal muscle. We first observed time-dependent increases (3-6 fold) of autophagy-related proteins (Atgs), including Ulk1, Beclin1 and LC3, along with reduced p62 expression during C2C12 differentiation, suggesting increased autophagy capacity and flux during myogenic differentiation. We then used cardiotoxin (CTX) or ischemia-reperfusion (IR) to induce muscle injury and regeneration and observed increases in Atgs between days 2-7 in adult skeletal muscle followed by increased autophagy flux after day 7. Since Ulk1 has been shown to be essential for mitophagy, we asked if Ulk1 is critical for functional regeneration in skeletal muscle. We subjected skeletal muscle-specific Ulk1 knockout mice (MKO) to CTX or IR. MKO mice had significantly impaired recovery of muscle strength and mitochondrial protein content post-CTX or IR. Imaging analysis showed that MKO mice have significantly attenuated recovery of mitochondrial network at 7 and 14 days post-CTX. These findings suggest that increased autophagy protein and flux occur during muscle regeneration, and Ulk1-mediated mitophagy is critical for recovery for mitochondrial network and hence functional regeneration.