Introduction: Congenital myasthenic syndromes (CMS) are rare inherited disorders of the neuromuscular junction caused by defects in synaptic transmission. They typically present in early infancy with hypotonia, ptosis, feeding difficulties, and recurrent respiratory failure. Early recognition is essential because several subtypes respond well to acetylcholinesterase inhibitors, resulting in significant functional improvement. Case presentation: We report a female infant, the third child of non-consanguineous parents, with a history of neonatal sibling death due to congenital heart disease. She underwent patent ductus arteriosus ligation at 42 days while on treatment for severe pneumonia complicated by heart failure, requiring prolonged mechanical ventilation with two failed extubations. At two months, she developed another severe pneumonia episode requiring one week of ventilatory support. Persistent generalized hypotonia, delayed gross motor development, dysphagia requiring nasogastric feeding from two months, and failure to thrive were noted. There was no tongue fasciculation or paradoxical breathing. Examination revealed bilateral ptosis, microphthalmia, and retinochoroidal coloboma. Serum creatine phosphokinase, thyroid function, metabolic profile, neuroimaging, electromyography, and nerve conduction studies were normal. Repetitive nerve stimulation showed a decremental response, and elevated acetylcholine receptor antibodies confirmed a neuromuscular junction disorder. Treatment with neostigmine and pyridostigmine resulted in marked improvement in tone, swallowing, and motor milestone acquisition. Genetic testing was not performed due to financial constraints. Conclusion: This case highlights the importance of considering CMS in infants with unexplained hypotonia and recurrent respiratory failure despite normal routine investigations. Early electrophysiological testing and timely initiation of acetylcholinesterase inhibitors can significantly improve neuromuscular function and developmental outcomes.