Neonatal thrombocytopenia is common and is frequently seen in neonatal sepsis. Drug-induced thrombocytopenia is likely to be missed unless a high index of suspicion is present. Changing of antibiotics for assumed nonresolution of sepsis may lead to persistent thrombocytopenia in a neonate if drug-induced thrombocytopenia is missed. Vancomycin-induced neonatal thrombocytopenia is rarely described in scientific literature. We describe a newborn who was diagnosed with early onset sepsis and vancomycin-induced thrombocytopenia. Other causes of thrombocytopenia such as sepsis, alloimmune thrombocytopenia, thrombosis etc. were excluded. The platelet counts normalized within 72 h of stopping vancomycin. Vancomycin-induced IgM platelet antibodies could not be done in our case (due to financial constraints), but their absence does not exclude the diagnosis of vancomycin-induced thrombocytopenia.