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Congenital thrombocytopenia results from genetic mutations in genes implicated in megakaryocyte differentiation and/or platelet formation and clearance. We report the case of an 11-month-old girl who presented with severe macrothrombocytopenia since birth and subsequently developed an intracranial bleed. She was diagnosed to have GNE gene mutation. GNE gene encodes the key enzyme in sialic acid biosynthesis, glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase (GNE/MNK). Its mutation is responsible for the reduction in sialic acid biosynthesis and consequently leads to severe congenital thrombocytopenia and/or myopathy. Although no sign of myopathy is observed in our patient; it is possible myopathy can be developed later, thus long-term follow-up with neurology is highly advisable. We recommend the genetic counseling and a segregation analysis of this variant in other affected individuals in the family.