Introduction: Congenital tuberculosis though rare is of paramount importance to outline early management. Symptoms of congenital tuberculosis may be present at birth but more commonly begin by second or third week of life. The clinical presentation of tuberculosis in newborns is similar to that caused by sepsis and other congenital infections. Purpose: Nonspecific nature of the disease in the newborn infant and less knowledge of the maternal disease prior to delivery makes the diagnosis a clinical challenge. Case report: A rare case of one and a half month F baby who had fever since 3 weeks of age, after a month baby landed into neonatal intensive care unit because of missed diagnosis and reported to us with clinical signs of sepsis. Investigations and results: X-Ray chest was suggestive of tuberculosis, presumptive diagnosis of tuberculosis made & baby started on anti tubercular therapy. Cartridge based nucleic acid amplification test was found positive in gastric aspirate. The baby started recovering and during that period mother developed symptoms of low grade fever, lethargy, headache and seizures. She was diagnosed as neurotuberculosis with evidence of multiple tuberculomas in MRI-Brain. This led to confirmation of diagnosis of congenital tuberculosis. Conclusion: Most important clue for rapid diagnosis of congenital tuberculosis is maternal history of tuberculosis. Often, the mother's disease is discovered after the neonatal diagnosis is suspected. In summary, there is need to improve screening to identify and treat active tuberculosis in prenatal period, which decreases perinatal mortality and prevents occurrence of this serious disease in neonate. This case remarks difficulties on diagnosis and therapeutic management about this important severe disease in public health, and alert for development of protocols that foresee these difficulties.