Muscular fatty infiltration is a common issue after rotator cuff tears (RCT) which impairs shoulder function. Females suffer higher prevalence and more severe degree of muscular fatty infiltration after RCT when compared to males, with the underlying mechanisms remaining unclear. Fibro/adipogenic progenitors (FAPs) are the primary source of muscular fatty infiltration following RCT. Our findings disclose that gender-specific disparities in muscular fatty infiltration are linked to mTOR/ULK1-mediated autophagy of FAPs. Decreased autophagic activity contributes to adipogenic differentiation in female FAPs after RCT. Furthermore, metformin could enhance mTOR/ULK1 mediated autophagic processes of FAPs, thereby alleviating fatty infiltration and improving shoulder functionality after RCT. Together, our study reveals that gender differences in muscular fatty infiltration arise from distinct autophagic activities. Metformin could be a promising non-invasive intervention to ameliorate muscular fatty infiltration of RCT.