Congenital myasthenic syndromes are clinically and genetically heterogeneous disorders characterized by a neuromuscular transmission defect. Mutations in novel genes have been described in recent years. Among these, MUSK gene mutations are extremely rare, with only 8 families identified worldwide to date. We report a Spanish case, a carrier of one known hetero-allelic missense mutation and one newly identified MUSK gene variant. Our patient presented with congenital onset ophthalmoplegia and palpebral ptosis associated with limb-girdle weakness and exercise intolerance without prominent fatigability, developed during his twenties. He was misdiagnosed as mitochondrial myopathy because of paraclinic and histologic findings, but detailed clinical examination prompted us to reassess him with repetitive stimulation technique, demonstrating decremental response and suggesting myasthenic syndrome. A genetic study confirmed the clinical diagnosis allowing us to started treatment with excellent clinical response.