Skeletal muscles undergo atrophy in response to diseases and aging. Here we report that mitofusin 2 (Mfn2) acts as a dominant suppressor of neuromuscular synaptic loss to preserve skeletal muscles. Mfn2 is reduced in spinal cords of transgenic SOD1G93A and aged mice. Through preserving neuromuscular synapses, increasing neuronal Mfn2 prevents skeletal muscle wasting in both SOD1G93A and aged mice, whereas deletion of neuronal Mfn2 produces neuromuscular synaptic dysfunction and skeletal muscle atrophy. Neuromuscular synaptic loss after sciatic nerve transection can also be alleviated by Mfn2. Mfn2 coexists with calpastatin largely in mitochondria-associated membranes (MAMs) to regulate its axonal transport. Genetic inactivation of calpastatin abolishes Mfn2-mediated protection of neuromuscular synapses. Our results suggest that, as a potential key component of a novel and heretofore unrecognized mechanism of cytoplasmic protein transport, Mfn2 may play a general role in preserving neuromuscular synapses and serve as a common therapeutic target for skeletal muscle atrophy. Display omitted •Mfn2 loss in neurons causes NMJ dysfunction and skeletal muscle atrophy•Mfn2 upregulation in neurons delays the disease onset in SOD1G93A mice by 68 days•Mfn2 in neurons protects NMJs in ALS, during aging, and upon nerve injury•Mfn2 in neurons regulates axonal transport of calpastatin to protect NMJs Wang et al. report on the unexpected function of the mitochondrial outer membrane protein mitofusin 2 (Mfn2) in mediating the axonal transport of calpastatin, which is involved in neuromuscular function, to protect neuromuscular synapses. Mfn2 overexpression can prevent neuromuscular synapse loss in amyotrophic lateral sclerosis (ALS) and aging-related sarcopenia.