Congenital myasthenic syndrome is difficult to diagnose, especially in the neonate when classic myasthenic signs may not be present. Congenital myasthenic syndrome with episodic apnea is a rare cause of recurrent apnea in infancy. We present an infant with nine severe episodes of apnea in her first 6 months who underwent a prolonged evaluation before ptosis was evident, leading to a diagnosis of choline acetyltransferase deficiency, a form of congenital myasthenic syndrome. Midazolam appeared to resolve the apnea on five occasions. The diagnosis was supported by edrophonium testing and repetitive nerve stimulation. Mutation analysis demonstrated compound heterozygous p.T354M and p.A557T mutations, the latter of which is novel. The patient's respiratory status stabilized on pyridostigmine, and she is ambulatory at age 3 years. Pyridostigmine is the primary therapy for choline acetyltransferase deficiency, but the efficacy of midazolam during this patient's episodes of apnea is interesting, and warrants further study.