Mitochondria play critical roles in maintaining oxidative metabolism and cardiac homeostasis; however, their function is compromised in aging hearts. Fibronectin type III domain-containing 4 (FNDC4) is involved in regulating mitochondrial biogenesis, energy expenditure, and metabolic balance. The present study found that aging mice exhibited a sizable decline in cardiac and plasma FNDC4 levels, and that lower FNDC4 expression also correlated with a poor cardiac function. Cardiac-specific FNDC4 overexpression alleviated, while cardiac-specific FNDC4 knockdown facilitated aging-related cardiac remodeling and dysfunction. The unbiased transcriptome analysis and untargeted metabolomics revealed that FNDC4 activated AMP-activated protein kinase α/peroxisome proliferator-activated receptor α signaling pathway to improve mitochondrial dysfunction and lipotoxicity in aging hearts.