Sarcopenia, the age-related decline in muscle mass and function, affects up to one-third of individuals over the age of 60. This condition contributes significantly to increased risk of falls, frailty, and mortality, and is partly driven by impaired muscle regeneration. Muscle stem cells (MuSCs) are critical for muscle repair, and targeting molecular regulators of muscle regeneration has emerged as a promising therapeutic strategy. However, the molecular mechanisms underlying this process remain complex and incompletely understood. Here, we identify Deformed Epidermal Autoregulatory Factor-1 (DEAF1) as a novel regulator of muscle regeneration. DEAF1 functions downstream of FOXO signaling and is transcriptionally repressed by FOXO proteins. We show that DEAF1 binds to the promoter regions of Pik3c3 and Atg16l1, suppressing their expression. Consequently, DEAF1 depletion activates macroautophagy/autophagy, which impairs MuSC survival and differentiation. Conversely, DEAF1 overexpression inhibits autophagy, leading to protein aggregation and MuSC death. Notably, both loss and overexpression of DEAF1 disrupt muscle regeneration, underscoring the need for precise regulation of DEAF1-mediated autophagy during this process. We further demonstrate that DEAF1 expression is altered with age, and its modulation can attenuate muscle atrophy and restore regenerative capacity in aged mice. Together, our findings reveal an evolutionarily conserved role for DEAF1 in regulating muscle regeneration through autophagy, offering new insights for therapeutic interventions targeting muscle atrophy in aging.